diff --git a/program/shinyApp/R/enrichment_analysis/enrichment_analysis.R b/program/shinyApp/R/enrichment_analysis/enrichment_analysis.R
index 0becf147..3ffad644 100644
--- a/program/shinyApp/R/enrichment_analysis/enrichment_analysis.R
+++ b/program/shinyApp/R/enrichment_analysis/enrichment_analysis.R
@@ -49,7 +49,7 @@ gene_set_enrichment <- function(
if(enrichments2do$KEGG){
if(
- !(identical(list("adjustMethod"=adjustMethod, "sort"=sorting),par_tmp[[session_key]]$EA[[comp_type]][[contrast]]$KEGG ))
+ !(identical(list("adjustMethod"=adjustMethod, "sort"=sorting),par_tmp[[session$token]]$EA[[comp_type]][[contrast]]$KEGG ))
){
genesets4ea <- msigdbr(
species = ifelse(input$OrganismChoice == "hsa","Homo sapiens","Mus musculus"),
@@ -64,15 +64,15 @@ gene_set_enrichment <- function(
pAdjustMethod = PADJUST_METHOD[[adjustMethod]],
pvalueCutoff = 1
)
- res_tmp[[session_key]]$EA[[comp_type]][[contrast]]$KEGG <<- EnrichmentRes_Kegg
- par_tmp[[session_key]]$EA[[comp_type]][[contrast]]$KEGG <<- list("adjustMethod"=adjustMethod, "sort"=sorting)
+ res_tmp[[session$token]]$EA[[comp_type]][[contrast]]$KEGG <<- EnrichmentRes_Kegg
+ par_tmp[[session$token]]$EA[[comp_type]][[contrast]]$KEGG <<- list("adjustMethod"=adjustMethod, "sort"=sorting)
}else{
- EnrichmentRes_Kegg <- res_tmp[[session_key]]$EA[[comp_type]][[contrast]]$KEGG
+ EnrichmentRes_Kegg <- res_tmp[[session$token]]$EA[[comp_type]][[contrast]]$KEGG
}
}
if(enrichments2do$GO){
if(
- !(identical(list("adjustMethod"=adjustMethod, "sort"=sorting),par_tmp[[session_key]]$EA[[comp_type]][[contrast]]$GO ))
+ !(identical(list("adjustMethod"=adjustMethod, "sort"=sorting),par_tmp[[session$token]]$EA[[comp_type]][[contrast]]$GO ))
){
EnrichmentRes_GO <- clusterProfiler::gseGO(
gene = geneSetChoice,
@@ -85,16 +85,16 @@ gene_set_enrichment <- function(
OrgDb = ifelse(input$OrganismChoice == "hsa","org.Hs.eg.db","org.Mm.eg.db"),
pAdjustMethod = "none" # TODO: discuss
)
- res_tmp[[session_key]]$EA[[comp_type]][[contrast]]$GO <<- EnrichmentRes_GO
- par_tmp[[session_key]]$EA[[comp_type]][[contrast]]$GO <<- list("adjustMethod"=adjustMethod, "sort"=sorting)
+ res_tmp[[session$token]]$EA[[comp_type]][[contrast]]$GO <<- EnrichmentRes_GO
+ par_tmp[[session$token]]$EA[[comp_type]][[contrast]]$GO <<- list("adjustMethod"=adjustMethod, "sort"=sorting)
}else{
- EnrichmentRes_GO <- res_tmp[[session_key]]$EA[[comp_type]][[contrast]]$GO
+ EnrichmentRes_GO <- res_tmp[[session$token]]$EA[[comp_type]][[contrast]]$GO
}
}
# Hallmarks
if(enrichments2do$Hallmarks){
if(
- !(identical(list("adjustMethod"=adjustMethod, "sort"=sorting),par_tmp[[session_key]]$EA[[comp_type]][[contrast]]$Hallmarks ))
+ !(identical(list("adjustMethod"=adjustMethod, "sort"=sorting),par_tmp[[session$token]]$EA[[comp_type]][[contrast]]$Hallmarks ))
){
Hallmarkset <- msigdbr(
species = ifelse(input$OrganismChoice == "hsa","Homo sapiens","Mus musculus"),
@@ -108,16 +108,16 @@ gene_set_enrichment <- function(
pAdjustMethod = PADJUST_METHOD[[adjustMethod]],
pvalueCutoff = 1
)
- res_tmp[[session_key]]$EA[[comp_type]][[contrast]]$Hallmarks <<- EnrichmentRes_Hallmarks
- par_tmp[[session_key]]$EA[[comp_type]][[contrast]]$Hallmarks <<- list("adjustMethod"=adjustMethod, "sort"=sorting)
+ res_tmp[[session$token]]$EA[[comp_type]][[contrast]]$Hallmarks <<- EnrichmentRes_Hallmarks
+ par_tmp[[session$token]]$EA[[comp_type]][[contrast]]$Hallmarks <<- list("adjustMethod"=adjustMethod, "sort"=sorting)
}else{
- EnrichmentRes_Hallmarks <- res_tmp[[session_key]]$EA[[comp_type]][[contrast]]$Hallmarks
+ EnrichmentRes_Hallmarks <- res_tmp[[session$token]]$EA[[comp_type]][[contrast]]$Hallmarks
}
}
# C1
if(enrichments2do$C1){
if(
- !(identical(list("adjustMethod"=adjustMethod, "sort"=sorting),par_tmp[[session_key]]$EA[[comp_type]][[contrast]]$C1 ))
+ !(identical(list("adjustMethod"=adjustMethod, "sort"=sorting),par_tmp[[session$token]]$EA[[comp_type]][[contrast]]$C1 ))
){
C1set <- msigdbr(
species = ifelse(input$OrganismChoice == "hsa","Homo sapiens","Mus musculus"),
@@ -131,17 +131,17 @@ gene_set_enrichment <- function(
pAdjustMethod = PADJUST_METHOD[[adjustMethod]],
pvalueCutoff = 1
)
- res_tmp[[session_key]]$EA[[comp_type]][[contrast]]$C1 <<- EnrichmentRes_C1
- par_tmp[[session_key]]$EA[[comp_type]][[contrast]]$C1 <<- list("adjustMethod"=adjustMethod, "sort"=sorting)
+ res_tmp[[session$token]]$EA[[comp_type]][[contrast]]$C1 <<- EnrichmentRes_C1
+ par_tmp[[session$token]]$EA[[comp_type]][[contrast]]$C1 <<- list("adjustMethod"=adjustMethod, "sort"=sorting)
}else{
- EnrichmentRes_C1 <- res_tmp[[session_key]]$EA[[comp_type]][[contrast]]$C1
+ EnrichmentRes_C1 <- res_tmp[[session$token]]$EA[[comp_type]][[contrast]]$C1
}
}
# C2
if(enrichments2do$C2){
if(
- !(identical(list("adjustMethod"=adjustMethod, "sort"=sorting),par_tmp[[session_key]]$EA[[comp_type]][[contrast]]$C2 ))
+ !(identical(list("adjustMethod"=adjustMethod, "sort"=sorting),par_tmp[[session$token]]$EA[[comp_type]][[contrast]]$C2 ))
){
C2set <- msigdbr(
species = ifelse(input$OrganismChoice == "hsa","Homo sapiens","Mus musculus"),
@@ -155,16 +155,16 @@ gene_set_enrichment <- function(
pAdjustMethod = PADJUST_METHOD[[adjustMethod]],
pvalueCutoff = 1
)
- res_tmp[[session_key]]$EA[[comp_type]][[contrast]]$C2 <<- EnrichmentRes_C2
- par_tmp[[session_key]]$EA[[comp_type]][[contrast]]$C2 <<- list("adjustMethod"=adjustMethod, "sort"=sorting)
+ res_tmp[[session$token]]$EA[[comp_type]][[contrast]]$C2 <<- EnrichmentRes_C2
+ par_tmp[[session$token]]$EA[[comp_type]][[contrast]]$C2 <<- list("adjustMethod"=adjustMethod, "sort"=sorting)
}else{
- EnrichmentRes_C2 <- res_tmp[[session_key]]$EA[[comp_type]][[contrast]]$C2
+ EnrichmentRes_C2 <- res_tmp[[session$token]]$EA[[comp_type]][[contrast]]$C2
}
}
# C3
if(enrichments2do$C3){
if(
- !(identical(list("adjustMethod"=adjustMethod, "sort"=sorting),par_tmp[[session_key]]$EA[[comp_type]][[contrast]]$C3 ))
+ !(identical(list("adjustMethod"=adjustMethod, "sort"=sorting),par_tmp[[session$token]]$EA[[comp_type]][[contrast]]$C3 ))
){
C3set <- msigdbr(
species = ifelse(input$OrganismChoice == "hsa","Homo sapiens","Mus musculus"),
@@ -178,16 +178,16 @@ gene_set_enrichment <- function(
pAdjustMethod = PADJUST_METHOD[[adjustMethod]],
pvalueCutoff = 1
)
- res_tmp[[session_key]]$EA[[comp_type]][[contrast]]$C3 <<- EnrichmentRes_C3
- par_tmp[[session_key]]$EA[[comp_type]][[contrast]]$C3 <<- list("adjustMethod"=adjustMethod, "sort"=sorting)
+ res_tmp[[session$token]]$EA[[comp_type]][[contrast]]$C3 <<- EnrichmentRes_C3
+ par_tmp[[session$token]]$EA[[comp_type]][[contrast]]$C3 <<- list("adjustMethod"=adjustMethod, "sort"=sorting)
}else{
- EnrichmentRes_C3 <- res_tmp[[session_key]]$EA[[comp_type]][[contrast]]$C3
+ EnrichmentRes_C3 <- res_tmp[[session$token]]$EA[[comp_type]][[contrast]]$C3
}
}
# C4
if(enrichments2do$C4){
if(
- !(identical(list("adjustMethod"=adjustMethod, "sort"=sorting),par_tmp[[session_key]]$EA[[comp_type]][[contrast]]$C4 ))
+ !(identical(list("adjustMethod"=adjustMethod, "sort"=sorting),par_tmp[[session$token]]$EA[[comp_type]][[contrast]]$C4 ))
){
C4set <- msigdbr(
species = ifelse(input$OrganismChoice == "hsa","Homo sapiens","Mus musculus"),
@@ -201,16 +201,16 @@ gene_set_enrichment <- function(
pAdjustMethod = PADJUST_METHOD[[adjustMethod]],
pvalueCutoff = 1
)
- res_tmp[[session_key]]$EA[[comp_type]][[contrast]]$C4 <<- EnrichmentRes_C4
- par_tmp[[session_key]]$EA[[comp_type]][[contrast]]$C4 <<- list("adjustMethod"=adjustMethod, "sort"=sorting)
+ res_tmp[[session$token]]$EA[[comp_type]][[contrast]]$C4 <<- EnrichmentRes_C4
+ par_tmp[[session$token]]$EA[[comp_type]][[contrast]]$C4 <<- list("adjustMethod"=adjustMethod, "sort"=sorting)
}else{
- EnrichmentRes_C4 <- res_tmp[[session_key]]$EA[[comp_type]][[contrast]]$C4
+ EnrichmentRes_C4 <- res_tmp[[session$token]]$EA[[comp_type]][[contrast]]$C4
}
}
# C5
if(enrichments2do$C5){
if(
- !(identical(list("adjustMethod"=adjustMethod, "sort"=sorting),par_tmp[[session_key]]$EA[[comp_type]][[contrast]]$C5 ))
+ !(identical(list("adjustMethod"=adjustMethod, "sort"=sorting),par_tmp[[session$token]]$EA[[comp_type]][[contrast]]$C5 ))
){
C5set <- msigdbr(
species = ifelse(input$OrganismChoice == "hsa","Homo sapiens","Mus musculus"),
@@ -224,16 +224,16 @@ gene_set_enrichment <- function(
pAdjustMethod = PADJUST_METHOD[[adjustMethod]],
pvalueCutoff = 1
)
- res_tmp[[session_key]]$EA[[comp_type]][[contrast]]$C5 <<- EnrichmentRes_C5
- par_tmp[[session_key]]$EA[[comp_type]][[contrast]]$C5 <<- list("adjustMethod"=adjustMethod, "sort"=sorting)
+ res_tmp[[session$token]]$EA[[comp_type]][[contrast]]$C5 <<- EnrichmentRes_C5
+ par_tmp[[session$token]]$EA[[comp_type]][[contrast]]$C5 <<- list("adjustMethod"=adjustMethod, "sort"=sorting)
}else{
- EnrichmentRes_C5 <- res_tmp[[session_key]]$EA[[comp_type]][[contrast]]$C5
+ EnrichmentRes_C5 <- res_tmp[[session$token]]$EA[[comp_type]][[contrast]]$C5
}
}
# C6
if(enrichments2do$C6){
if(
- !(identical(list("adjustMethod"=adjustMethod, "sort"=sorting),par_tmp[[session_key]]$EA[[comp_type]][[contrast]]$C6 ))
+ !(identical(list("adjustMethod"=adjustMethod, "sort"=sorting),par_tmp[[session$token]]$EA[[comp_type]][[contrast]]$C6 ))
){
C6set <- msigdbr(
species = ifelse(input$OrganismChoice == "hsa","Homo sapiens","Mus musculus"),
@@ -247,16 +247,16 @@ gene_set_enrichment <- function(
pAdjustMethod = PADJUST_METHOD[[adjustMethod]],
pvalueCutoff = 1
)
- res_tmp[[session_key]]$EA[[comp_type]][[contrast]]$C6 <<- EnrichmentRes_C6
- par_tmp[[session_key]]$EA[[comp_type]][[contrast]]$C6 <<- list("adjustMethod"=adjustMethod, "sort"=sorting)
+ res_tmp[[session$token]]$EA[[comp_type]][[contrast]]$C6 <<- EnrichmentRes_C6
+ par_tmp[[session$token]]$EA[[comp_type]][[contrast]]$C6 <<- list("adjustMethod"=adjustMethod, "sort"=sorting)
}else{
- EnrichmentRes_C6 <- res_tmp[[session_key]]$EA[[comp_type]][[contrast]]$C6
+ EnrichmentRes_C6 <- res_tmp[[session$token]]$EA[[comp_type]][[contrast]]$C6
}
}
# C7
if(enrichments2do$C7){
if(
- !(identical(list("adjustMethod"=adjustMethod, "sort"=sorting),par_tmp[[session_key]]$EA[[comp_type]][[contrast]]$C7 ))
+ !(identical(list("adjustMethod"=adjustMethod, "sort"=sorting),par_tmp[[session$token]]$EA[[comp_type]][[contrast]]$C7 ))
){
genesets4ea <- msigdbr(
species = ifelse(input$OrganismChoice == "hsa","Homo sapiens","Mus musculus"),
@@ -270,16 +270,16 @@ gene_set_enrichment <- function(
pAdjustMethod = PADJUST_METHOD[[adjustMethod]],
pvalueCutoff = 1
)
- res_tmp[[session_key]]$EA[[comp_type]][[contrast]]$C7 <<- EnrichmentRes_C7
- par_tmp[[session_key]]$EA[[comp_type]][[contrast]]$C7 <<- list("adjustMethod"=adjustMethod, "sort"=sorting)
+ res_tmp[[session$token]]$EA[[comp_type]][[contrast]]$C7 <<- EnrichmentRes_C7
+ par_tmp[[session$token]]$EA[[comp_type]][[contrast]]$C7 <<- list("adjustMethod"=adjustMethod, "sort"=sorting)
}else{
- EnrichmentRes_C7 <- res_tmp[[session_key]]$EA[[comp_type]][[contrast]]$C7
+ EnrichmentRes_C7 <- res_tmp[[session$token]]$EA[[comp_type]][[contrast]]$C7
}
}
# C8
if(enrichments2do$C8){
if(
- !(identical(list("adjustMethod"=adjustMethod, "sort"=sorting),par_tmp[[session_key]]$EA[[comp_type]][[contrast]]$C8 ))
+ !(identical(list("adjustMethod"=adjustMethod, "sort"=sorting),par_tmp[[session$token]]$EA[[comp_type]][[contrast]]$C8 ))
){
C8set <- msigdbr(
species = ifelse(input$OrganismChoice == "hsa","Homo sapiens","Mus musculus"),
@@ -293,16 +293,16 @@ gene_set_enrichment <- function(
pAdjustMethod = PADJUST_METHOD[[adjustMethod]],
pvalueCutoff = 1
)
- res_tmp[[session_key]]$EA[[comp_type]][[contrast]]$C8 <<- EnrichmentRes_C8
- par_tmp[[session_key]]$EA[[comp_type]][[contrast]]$C8 <<- list("adjustMethod"=adjustMethod, "sort"=sorting)
+ res_tmp[[session$token]]$EA[[comp_type]][[contrast]]$C8 <<- EnrichmentRes_C8
+ par_tmp[[session$token]]$EA[[comp_type]][[contrast]]$C8 <<- list("adjustMethod"=adjustMethod, "sort"=sorting)
}else{
- EnrichmentRes_C8 <- res_tmp[[session_key]]$EA[[comp_type]][[contrast]]$C8
+ EnrichmentRes_C8 <- res_tmp[[session$token]]$EA[[comp_type]][[contrast]]$C8
}
}
# C2 subset CGP
if(enrichments2do$CGP){
if(
- !(identical(list("adjustMethod"=adjustMethod, "sort"=sorting),par_tmp[[session_key]]$EA[[comp_type]][[contrast]]$CGP ))
+ !(identical(list("adjustMethod"=adjustMethod, "sort"=sorting),par_tmp[[session$token]]$EA[[comp_type]][[contrast]]$CGP ))
){
genesets4ea <- msigdbr(
species = ifelse(input$OrganismChoice == "hsa","Homo sapiens","Mus musculus"),
@@ -317,16 +317,16 @@ gene_set_enrichment <- function(
pAdjustMethod = PADJUST_METHOD[[adjustMethod]],
pvalueCutoff = 1
)
- res_tmp[[session_key]]$EA[[comp_type]][[contrast]]$CGP <<- EnrichmentRes_CGP
- par_tmp[[session_key]]$EA[[comp_type]][[contrast]]$CGP <<- list("adjustMethod"=adjustMethod, "sort"=sorting)
+ res_tmp[[session$token]]$EA[[comp_type]][[contrast]]$CGP <<- EnrichmentRes_CGP
+ par_tmp[[session$token]]$EA[[comp_type]][[contrast]]$CGP <<- list("adjustMethod"=adjustMethod, "sort"=sorting)
}else{
- EnrichmentRes_CGP <- res_tmp[[session_key]]$EA[[comp_type]][[contrast]]$CGP
+ EnrichmentRes_CGP <- res_tmp[[session$token]]$EA[[comp_type]][[contrast]]$CGP
}
}
# C2 subset CP
if(enrichments2do$CP){
if(
- !(identical(list("adjustMethod"=adjustMethod, "sort"=sorting),par_tmp[[session_key]]$EA[[comp_type]][[contrast]]$CP ))
+ !(identical(list("adjustMethod"=adjustMethod, "sort"=sorting),par_tmp[[session$token]]$EA[[comp_type]][[contrast]]$CP ))
){
genesets4ea <- msigdbr(
species = ifelse(input$OrganismChoice == "hsa","Homo sapiens","Mus musculus"),
@@ -341,16 +341,16 @@ gene_set_enrichment <- function(
pAdjustMethod = PADJUST_METHOD[[adjustMethod]],
pvalueCutoff = 1
)
- res_tmp[[session_key]]$EA[[comp_type]][[contrast]]$CP <<- EnrichmentRes_CP
- par_tmp[[session_key]]$EA[[comp_type]][[contrast]]$CP <<- list("adjustMethod"=adjustMethod, "sort"=sorting)
+ res_tmp[[session$token]]$EA[[comp_type]][[contrast]]$CP <<- EnrichmentRes_CP
+ par_tmp[[session$token]]$EA[[comp_type]][[contrast]]$CP <<- list("adjustMethod"=adjustMethod, "sort"=sorting)
}else{
- EnrichmentRes_CP <- res_tmp[[session_key]]$EA[[comp_type]][[contrast]]$CP
+ EnrichmentRes_CP <- res_tmp[[session$token]]$EA[[comp_type]][[contrast]]$CP
}
}
# C2:CP subset BIOCARTA
if(enrichments2do$BIOCARTA){
if(
- !(identical(list("adjustMethod"=adjustMethod, "sort"=sorting),par_tmp[[session_key]]$EA[[comp_type]][[contrast]]$BIOCARTA ))
+ !(identical(list("adjustMethod"=adjustMethod, "sort"=sorting),par_tmp[[session$token]]$EA[[comp_type]][[contrast]]$BIOCARTA ))
){
genesets4ea <- msigdbr(
species = ifelse(input$OrganismChoice == "hsa","Homo sapiens","Mus musculus"),
@@ -365,16 +365,16 @@ gene_set_enrichment <- function(
pAdjustMethod = PADJUST_METHOD[[adjustMethod]],
pvalueCutoff = 1
)
- res_tmp[[session_key]]$EA[[comp_type]][[contrast]]$BIOCARTA <<- EnrichmentRes_BIOCARTA
- par_tmp[[session_key]]$EA[[comp_type]][[contrast]]$BIOCARTA <<- list("adjustMethod"=adjustMethod, "sort"=sorting)
+ res_tmp[[session$token]]$EA[[comp_type]][[contrast]]$BIOCARTA <<- EnrichmentRes_BIOCARTA
+ par_tmp[[session$token]]$EA[[comp_type]][[contrast]]$BIOCARTA <<- list("adjustMethod"=adjustMethod, "sort"=sorting)
}else{
- EnrichmentRes_BIOCARTA <- res_tmp[[session_key]]$EA[[comp_type]][[contrast]]$BIOCARTA
+ EnrichmentRes_BIOCARTA <- res_tmp[[session$token]]$EA[[comp_type]][[contrast]]$BIOCARTA
}
}
# C2:CP subset PID
if(enrichments2do$PID){
if(
- !(identical(list("adjustMethod"=adjustMethod, "sort"=sorting),par_tmp[[session_key]]$EA[[comp_type]][[contrast]]$PID ))
+ !(identical(list("adjustMethod"=adjustMethod, "sort"=sorting),par_tmp[[session$token]]$EA[[comp_type]][[contrast]]$PID ))
){
genesets4ea <- msigdbr(
species = ifelse(input$OrganismChoice == "hsa","Homo sapiens","Mus musculus"),
@@ -389,16 +389,16 @@ gene_set_enrichment <- function(
pAdjustMethod = PADJUST_METHOD[[adjustMethod]],
pvalueCutoff = 1
)
- res_tmp[[session_key]]$EA[[comp_type]][[contrast]]$PID <<- EnrichmentRes_PID
- par_tmp[[session_key]]$EA[[comp_type]][[contrast]]$PID <<- list("adjustMethod"=adjustMethod, "sort"=sorting)
+ res_tmp[[session$token]]$EA[[comp_type]][[contrast]]$PID <<- EnrichmentRes_PID
+ par_tmp[[session$token]]$EA[[comp_type]][[contrast]]$PID <<- list("adjustMethod"=adjustMethod, "sort"=sorting)
}else{
- EnrichmentRes_PID <- res_tmp[[session_key]]$EA[[comp_type]][[contrast]]$PID
+ EnrichmentRes_PID <- res_tmp[[session$token]]$EA[[comp_type]][[contrast]]$PID
}
}
# C2:CP subset REACTOME
if(enrichments2do$REACTOME){
if(
- !(identical(list("adjustMethod"=adjustMethod, "sort"=sorting),par_tmp[[session_key]]$EA[[comp_type]][[contrast]]$REACTOME ))
+ !(identical(list("adjustMethod"=adjustMethod, "sort"=sorting),par_tmp[[session$token]]$EA[[comp_type]][[contrast]]$REACTOME ))
){
genesets4ea <- msigdbr(
species = ifelse(input$OrganismChoice == "hsa","Homo sapiens","Mus musculus"),
@@ -413,16 +413,16 @@ gene_set_enrichment <- function(
pAdjustMethod = PADJUST_METHOD[[adjustMethod]],
pvalueCutoff = 1
)
- res_tmp[[session_key]]$EA[[comp_type]][[contrast]]$REACTOME <<- EnrichmentRes_REACTOME
- par_tmp[[session_key]]$EA[[comp_type]][[contrast]]$REACTOME <<- list("adjustMethod"=adjustMethod, "sort"=sorting)
+ res_tmp[[session$token]]$EA[[comp_type]][[contrast]]$REACTOME <<- EnrichmentRes_REACTOME
+ par_tmp[[session$token]]$EA[[comp_type]][[contrast]]$REACTOME <<- list("adjustMethod"=adjustMethod, "sort"=sorting)
}else{
- EnrichmentRes_REACTOME <- res_tmp[[session_key]]$EA[[comp_type]][[contrast]]$REACTOME
+ EnrichmentRes_REACTOME <- res_tmp[[session$token]]$EA[[comp_type]][[contrast]]$REACTOME
}
}
# C2:CP subset WIKIPATHWAYS
if(enrichments2do$WIKIPATHWAYS){
if(
- !(identical(list("adjustMethod"=adjustMethod, "sort"=sorting),par_tmp[[session_key]]$EA[[comp_type]][[contrast]]$WIKIPATHWAYS ))
+ !(identical(list("adjustMethod"=adjustMethod, "sort"=sorting),par_tmp[[session$token]]$EA[[comp_type]][[contrast]]$WIKIPATHWAYS ))
){
genesets4ea <- msigdbr(
species = ifelse(input$OrganismChoice == "hsa","Homo sapiens","Mus musculus"),
@@ -437,16 +437,16 @@ gene_set_enrichment <- function(
pAdjustMethod = PADJUST_METHOD[[adjustMethod]],
pvalueCutoff = 1
)
- res_tmp[[session_key]]$EA[[comp_type]][[contrast]]$WIKIPATHWAYS <<- EnrichmentRes_WIKIPATHWAYS
- par_tmp[[session_key]]$EA[[comp_type]][[contrast]]$WIKIPATHWAYS <<- list("adjustMethod"=adjustMethod, "sort"=sorting)
+ res_tmp[[session$token]]$EA[[comp_type]][[contrast]]$WIKIPATHWAYS <<- EnrichmentRes_WIKIPATHWAYS
+ par_tmp[[session$token]]$EA[[comp_type]][[contrast]]$WIKIPATHWAYS <<- list("adjustMethod"=adjustMethod, "sort"=sorting)
}else{
- EnrichmentRes_WIKIPATHWAYS <- res_tmp[[session_key]]$EA[[comp_type]][[contrast]]$WIKIPATHWAYS
+ EnrichmentRes_WIKIPATHWAYS <- res_tmp[[session$token]]$EA[[comp_type]][[contrast]]$WIKIPATHWAYS
}
}
# C3 subset MIR:MIRDB
if(enrichments2do$MIRDB){
if(
- !(identical(list("adjustMethod"=adjustMethod, "sort"=sorting),par_tmp[[session_key]]$EA[[comp_type]][[contrast]]$MIRDB ))
+ !(identical(list("adjustMethod"=adjustMethod, "sort"=sorting),par_tmp[[session$token]]$EA[[comp_type]][[contrast]]$MIRDB ))
){
genesets4ea <- msigdbr(
species = ifelse(input$OrganismChoice == "hsa","Homo sapiens","Mus musculus"),
@@ -461,16 +461,16 @@ gene_set_enrichment <- function(
pAdjustMethod = PADJUST_METHOD[[adjustMethod]],
pvalueCutoff = 1
)
- res_tmp[[session_key]]$EA[[comp_type]][[contrast]]$MIRDB <<- EnrichmentRes_MIRDB
- par_tmp[[session_key]]$EA[[comp_type]][[contrast]]$MIRDB <<- list("adjustMethod"=adjustMethod, "sort"=sorting)
+ res_tmp[[session$token]]$EA[[comp_type]][[contrast]]$MIRDB <<- EnrichmentRes_MIRDB
+ par_tmp[[session$token]]$EA[[comp_type]][[contrast]]$MIRDB <<- list("adjustMethod"=adjustMethod, "sort"=sorting)
}else{
- EnrichmentRes_MIRDB <- res_tmp[[session_key]]$EA[[comp_type]][[contrast]]$MIRDB
+ EnrichmentRes_MIRDB <- res_tmp[[session$token]]$EA[[comp_type]][[contrast]]$MIRDB
}
}
# C3 subset MIR:MIR_Legacy
if(enrichments2do$MIR_Legacy){
if(
- !(identical(list("adjustMethod"=adjustMethod, "sort"=sorting),par_tmp[[session_key]]$EA[[comp_type]][[contrast]]$MIR_Legacy ))
+ !(identical(list("adjustMethod"=adjustMethod, "sort"=sorting),par_tmp[[session$token]]$EA[[comp_type]][[contrast]]$MIR_Legacy ))
){
genesets4ea <- msigdbr(
species = ifelse(input$OrganismChoice == "hsa","Homo sapiens","Mus musculus"),
@@ -485,16 +485,16 @@ gene_set_enrichment <- function(
pAdjustMethod = PADJUST_METHOD[[adjustMethod]],
pvalueCutoff = 1
)
- res_tmp[[session_key]]$EA[[comp_type]][[contrast]]$MIR_Legacy <<- EnrichmentRes_MIR_Legacy
- par_tmp[[session_key]]$EA[[comp_type]][[contrast]]$MIR_Legacy <<- list("adjustMethod"=adjustMethod, "sort"=sorting)
+ res_tmp[[session$token]]$EA[[comp_type]][[contrast]]$MIR_Legacy <<- EnrichmentRes_MIR_Legacy
+ par_tmp[[session$token]]$EA[[comp_type]][[contrast]]$MIR_Legacy <<- list("adjustMethod"=adjustMethod, "sort"=sorting)
}else{
- EnrichmentRes_MIR_Legacy <- res_tmp[[session_key]]$EA[[comp_type]][[contrast]]$MIR_Legacy
+ EnrichmentRes_MIR_Legacy <- res_tmp[[session$token]]$EA[[comp_type]][[contrast]]$MIR_Legacy
}
}
# C3 subset TFT:GTRD
if(enrichments2do$GTRD){
if(
- !(identical(list("adjustMethod"=adjustMethod, "sort"=sorting),par_tmp[[session_key]]$EA[[comp_type]][[contrast]]$GTRD ))
+ !(identical(list("adjustMethod"=adjustMethod, "sort"=sorting),par_tmp[[session$token]]$EA[[comp_type]][[contrast]]$GTRD ))
){
genesets4ea <- msigdbr(
species = ifelse(input$OrganismChoice == "hsa","Homo sapiens","Mus musculus"),
@@ -509,16 +509,16 @@ gene_set_enrichment <- function(
pAdjustMethod = PADJUST_METHOD[[adjustMethod]],
pvalueCutoff = 1
)
- res_tmp[[session_key]]$EA[[comp_type]][[contrast]]$GTRD <<- EnrichmentRes_GTRD
- par_tmp[[session_key]]$EA[[comp_type]][[contrast]]$GTRD <<- list("adjustMethod"=adjustMethod, "sort"=sorting)
+ res_tmp[[session$token]]$EA[[comp_type]][[contrast]]$GTRD <<- EnrichmentRes_GTRD
+ par_tmp[[session$token]]$EA[[comp_type]][[contrast]]$GTRD <<- list("adjustMethod"=adjustMethod, "sort"=sorting)
}else{
- EnrichmentRes_GTRD <- res_tmp[[session_key]]$EA[[comp_type]][[contrast]]$GTRD
+ EnrichmentRes_GTRD <- res_tmp[[session$token]]$EA[[comp_type]][[contrast]]$GTRD
}
}
# C3 subset TFT:TFT_Legacy
if(enrichments2do$TFT_Legacy){
if(
- !(identical(list("adjustMethod"=adjustMethod, "sort"=sorting),par_tmp[[session_key]]$EA[[comp_type]][[contrast]]$TFT_Legacy ))
+ !(identical(list("adjustMethod"=adjustMethod, "sort"=sorting),par_tmp[[session$token]]$EA[[comp_type]][[contrast]]$TFT_Legacy ))
){
genesets4ea <- msigdbr(
species = ifelse(input$OrganismChoice == "hsa","Homo sapiens","Mus musculus"),
@@ -533,16 +533,16 @@ gene_set_enrichment <- function(
pAdjustMethod = PADJUST_METHOD[[adjustMethod]],
pvalueCutoff = 1
)
- res_tmp[[session_key]]$EA[[comp_type]][[contrast]]$TFT_Legacy <<- EnrichmentRes_TFT_Legacy
- par_tmp[[session_key]]$EA[[comp_type]][[contrast]]$TFT_Legacy <<- list("adjustMethod"=adjustMethod, "sort"=sorting)
+ res_tmp[[session$token]]$EA[[comp_type]][[contrast]]$TFT_Legacy <<- EnrichmentRes_TFT_Legacy
+ par_tmp[[session$token]]$EA[[comp_type]][[contrast]]$TFT_Legacy <<- list("adjustMethod"=adjustMethod, "sort"=sorting)
}else{
- EnrichmentRes_TFT_Legacy <- res_tmp[[session_key]]$EA[[comp_type]][[contrast]]$TFT_Legacy
+ EnrichmentRes_TFT_Legacy <- res_tmp[[session$token]]$EA[[comp_type]][[contrast]]$TFT_Legacy
}
}
# C4 subset CGN
if(enrichments2do$CGN){
if(
- !(identical(list("adjustMethod"=adjustMethod, "sort"=sorting),par_tmp[[session_key]]$EA[[comp_type]][[contrast]]$CGN ))
+ !(identical(list("adjustMethod"=adjustMethod, "sort"=sorting),par_tmp[[session$token]]$EA[[comp_type]][[contrast]]$CGN ))
){
genesets4ea <- msigdbr(
species = ifelse(input$OrganismChoice == "hsa","Homo sapiens","Mus musculus"),
@@ -557,16 +557,16 @@ gene_set_enrichment <- function(
pAdjustMethod = PADJUST_METHOD[[adjustMethod]],
pvalueCutoff = 1
)
- res_tmp[[session_key]]$EA[[comp_type]][[contrast]]$CGN <<- EnrichmentRes_CGN
- par_tmp[[session_key]]$EA[[comp_type]][[contrast]]$CGN <<- list("adjustMethod"=adjustMethod, "sort"=sorting)
+ res_tmp[[session$token]]$EA[[comp_type]][[contrast]]$CGN <<- EnrichmentRes_CGN
+ par_tmp[[session$token]]$EA[[comp_type]][[contrast]]$CGN <<- list("adjustMethod"=adjustMethod, "sort"=sorting)
}else{
- EnrichmentRes_CGN <- res_tmp[[session_key]]$EA[[comp_type]][[contrast]]$CGN
+ EnrichmentRes_CGN <- res_tmp[[session$token]]$EA[[comp_type]][[contrast]]$CGN
}
}
# C4 subset CM
if(enrichments2do$CM){
if(
- !(identical(list("adjustMethod"=adjustMethod, "sort"=sorting),par_tmp[[session_key]]$EA[[comp_type]][[contrast]]$CM ))
+ !(identical(list("adjustMethod"=adjustMethod, "sort"=sorting),par_tmp[[session$token]]$EA[[comp_type]][[contrast]]$CM ))
){
genesets4ea <- msigdbr(
species = ifelse(input$OrganismChoice == "hsa","Homo sapiens","Mus musculus"),
@@ -581,16 +581,16 @@ gene_set_enrichment <- function(
pAdjustMethod = PADJUST_METHOD[[adjustMethod]],
pvalueCutoff = 1
)
- res_tmp[[session_key]]$EA[[comp_type]][[contrast]]$CM <<- EnrichmentRes_CM
- par_tmp[[session_key]]$EA[[comp_type]][[contrast]]$CM <<- list("adjustMethod"=adjustMethod, "sort"=sorting)
+ res_tmp[[session$token]]$EA[[comp_type]][[contrast]]$CM <<- EnrichmentRes_CM
+ par_tmp[[session$token]]$EA[[comp_type]][[contrast]]$CM <<- list("adjustMethod"=adjustMethod, "sort"=sorting)
}else{
- EnrichmentRes_CM <- res_tmp[[session_key]]$EA[[comp_type]][[contrast]]$CM
+ EnrichmentRes_CM <- res_tmp[[session$token]]$EA[[comp_type]][[contrast]]$CM
}
}
# C5 subset GO BP
if(enrichments2do$GO_BP){
if(
- !(identical(list("adjustMethod"=adjustMethod, "sort"=sorting),par_tmp[[session_key]]$EA[[comp_type]][[contrast]]$GO_BP ))
+ !(identical(list("adjustMethod"=adjustMethod, "sort"=sorting),par_tmp[[session$token]]$EA[[comp_type]][[contrast]]$GO_BP ))
){
genesets4ea <- msigdbr(
species = ifelse(input$OrganismChoice == "hsa","Homo sapiens","Mus musculus"),
@@ -605,16 +605,16 @@ gene_set_enrichment <- function(
pAdjustMethod = PADJUST_METHOD[[adjustMethod]],
pvalueCutoff = 1
)
- res_tmp[[session_key]]$EA[[comp_type]][[contrast]]$GO_BP <<- EnrichmentRes_GO_BP
- par_tmp[[session_key]]$EA[[comp_type]][[contrast]]$GO_BP <<- list("adjustMethod"=adjustMethod, "sort"=sorting)
+ res_tmp[[session$token]]$EA[[comp_type]][[contrast]]$GO_BP <<- EnrichmentRes_GO_BP
+ par_tmp[[session$token]]$EA[[comp_type]][[contrast]]$GO_BP <<- list("adjustMethod"=adjustMethod, "sort"=sorting)
}else{
- EnrichmentRes_GO_BP <- res_tmp[[session_key]]$EA[[comp_type]][[contrast]]$GO_BP
+ EnrichmentRes_GO_BP <- res_tmp[[session$token]]$EA[[comp_type]][[contrast]]$GO_BP
}
}
# C5 subset GO CC
if(enrichments2do$GO_CC){
if(
- !(identical(list("adjustMethod"=adjustMethod, "sort"=sorting),par_tmp[[session_key]]$EA[[comp_type]][[contrast]]$GO_CC ))
+ !(identical(list("adjustMethod"=adjustMethod, "sort"=sorting),par_tmp[[session$token]]$EA[[comp_type]][[contrast]]$GO_CC ))
){
genesets4ea <- msigdbr(
species = ifelse(input$OrganismChoice == "hsa","Homo sapiens","Mus musculus"),
@@ -629,16 +629,16 @@ gene_set_enrichment <- function(
pAdjustMethod = PADJUST_METHOD[[adjustMethod]],
pvalueCutoff = 1
)
- res_tmp[[session_key]]$EA[[comp_type]][[contrast]]$GO_CC <<- EnrichmentRes_GO_CC
- par_tmp[[session_key]]$EA[[comp_type]][[contrast]]$GO_CC <<- list("adjustMethod"=adjustMethod, "sort"=sorting)
+ res_tmp[[session$token]]$EA[[comp_type]][[contrast]]$GO_CC <<- EnrichmentRes_GO_CC
+ par_tmp[[session$token]]$EA[[comp_type]][[contrast]]$GO_CC <<- list("adjustMethod"=adjustMethod, "sort"=sorting)
}else{
- EnrichmentRes_GO_CC <- res_tmp[[session_key]]$EA[[comp_type]][[contrast]]$GO_CC
+ EnrichmentRes_GO_CC <- res_tmp[[session$token]]$EA[[comp_type]][[contrast]]$GO_CC
}
}
# C5 subset GO MF
if(enrichments2do$GO_MF){
if(
- !(identical(list("adjustMethod"=adjustMethod, "sort"=sorting),par_tmp[[session_key]]$EA[[comp_type]][[contrast]]$GO_MF ))
+ !(identical(list("adjustMethod"=adjustMethod, "sort"=sorting),par_tmp[[session$token]]$EA[[comp_type]][[contrast]]$GO_MF ))
){
genesets4ea <- msigdbr(
species = ifelse(input$OrganismChoice == "hsa","Homo sapiens","Mus musculus"),
@@ -653,16 +653,16 @@ gene_set_enrichment <- function(
pAdjustMethod = PADJUST_METHOD[[adjustMethod]],
pvalueCutoff = 1
)
- res_tmp[[session_key]]$EA[[comp_type]][[contrast]]$GO_MF <<- EnrichmentRes_GO_MF
- par_tmp[[session_key]]$EA[[comp_type]][[contrast]]$GO_MF <<- list("adjustMethod"=adjustMethod, "sort"=sorting)
+ res_tmp[[session$token]]$EA[[comp_type]][[contrast]]$GO_MF <<- EnrichmentRes_GO_MF
+ par_tmp[[session$token]]$EA[[comp_type]][[contrast]]$GO_MF <<- list("adjustMethod"=adjustMethod, "sort"=sorting)
}else{
- EnrichmentRes_GO_MF <- res_tmp[[session_key]]$EA[[comp_type]][[contrast]]$GO_MF
+ EnrichmentRes_GO_MF <- res_tmp[[session$token]]$EA[[comp_type]][[contrast]]$GO_MF
}
}
# C5 subset HPO
if(enrichments2do$HPO){
if(
- !(identical(list("adjustMethod"=adjustMethod, "sort"=sorting),par_tmp[[session_key]]$EA[[comp_type]][[contrast]]$HPO ))
+ !(identical(list("adjustMethod"=adjustMethod, "sort"=sorting),par_tmp[[session$token]]$EA[[comp_type]][[contrast]]$HPO ))
){
genesets4ea <- msigdbr(
species = ifelse(input$OrganismChoice == "hsa","Homo sapiens","Mus musculus"),
@@ -677,16 +677,16 @@ gene_set_enrichment <- function(
pAdjustMethod = PADJUST_METHOD[[adjustMethod]],
pvalueCutoff = 1
)
- res_tmp[[session_key]]$EA[[comp_type]][[contrast]]$HPO <<- EnrichmentRes_HPO
- par_tmp[[session_key]]$EA[[comp_type]][[contrast]]$HPO <<- list("adjustMethod"=adjustMethod, "sort"=sorting)
+ res_tmp[[session$token]]$EA[[comp_type]][[contrast]]$HPO <<- EnrichmentRes_HPO
+ par_tmp[[session$token]]$EA[[comp_type]][[contrast]]$HPO <<- list("adjustMethod"=adjustMethod, "sort"=sorting)
}else{
- EnrichmentRes_HPO <- res_tmp[[session_key]]$EA[[comp_type]][[contrast]]$HPO
+ EnrichmentRes_HPO <- res_tmp[[session$token]]$EA[[comp_type]][[contrast]]$HPO
}
}
# C7 subset IMMUNESIGDB
if(enrichments2do$IMMUNESIGDB){
if(
- !(identical(list("adjustMethod"=adjustMethod, "sort"=sorting),par_tmp[[session_key]]$EA[[comp_type]][[contrast]]$IMMUNESIGDB ))
+ !(identical(list("adjustMethod"=adjustMethod, "sort"=sorting),par_tmp[[session$token]]$EA[[comp_type]][[contrast]]$IMMUNESIGDB ))
){
genesets4ea <- msigdbr(
species = ifelse(input$OrganismChoice == "hsa","Homo sapiens","Mus musculus"),
@@ -701,16 +701,16 @@ gene_set_enrichment <- function(
pAdjustMethod = PADJUST_METHOD[[adjustMethod]],
pvalueCutoff = 1
)
- res_tmp[[session_key]]$EA[[comp_type]][[contrast]]$IMMUNESIGDB <<- EnrichmentRes_IMMUNESIGDB
- par_tmp[[session_key]]$EA[[comp_type]][[contrast]]$IMMUNESIGDB <<- list("adjustMethod"=adjustMethod, "sort"=sorting)
+ res_tmp[[session$token]]$EA[[comp_type]][[contrast]]$IMMUNESIGDB <<- EnrichmentRes_IMMUNESIGDB
+ par_tmp[[session$token]]$EA[[comp_type]][[contrast]]$IMMUNESIGDB <<- list("adjustMethod"=adjustMethod, "sort"=sorting)
}else{
- EnrichmentRes_IMMUNESIGDB <- res_tmp[[session_key]]$EA[[comp_type]][[contrast]]$IMMUNESIGDB
+ EnrichmentRes_IMMUNESIGDB <- res_tmp[[session$token]]$EA[[comp_type]][[contrast]]$IMMUNESIGDB
}
}
# C7 subset VAX
if(enrichments2do$VAX){
if(
- !(identical(list("adjustMethod"=adjustMethod, "sort"=sorting),par_tmp[[session_key]]$EA[[comp_type]][[contrast]]$VAX ))
+ !(identical(list("adjustMethod"=adjustMethod, "sort"=sorting),par_tmp[[session$token]]$EA[[comp_type]][[contrast]]$VAX ))
){
genesets4ea <- msigdbr(
species = ifelse(input$OrganismChoice == "hsa","Homo sapiens","Mus musculus"),
@@ -725,10 +725,10 @@ gene_set_enrichment <- function(
pAdjustMethod = PADJUST_METHOD[[adjustMethod]],
pvalueCutoff = 1
)
- res_tmp[[session_key]]$EA[[comp_type]][[contrast]]$VAX <<- EnrichmentRes_VAX
- par_tmp[[session_key]]$EA[[comp_type]][[contrast]]$VAX <<- list("adjustMethod"=adjustMethod, "sort"=sorting)
+ res_tmp[[session$token]]$EA[[comp_type]][[contrast]]$VAX <<- EnrichmentRes_VAX
+ par_tmp[[session$token]]$EA[[comp_type]][[contrast]]$VAX <<- list("adjustMethod"=adjustMethod, "sort"=sorting)
}else{
- EnrichmentRes_VAX <- res_tmp[[session_key]]$EA[[comp_type]][[contrast]]$VAX
+ EnrichmentRes_VAX <- res_tmp[[session$token]]$EA[[comp_type]][[contrast]]$VAX
}
}
diff --git a/program/shinyApp/R/enrichment_analysis/overrepresentation_analysis.R b/program/shinyApp/R/enrichment_analysis/overrepresentation_analysis.R
index b44aa296..1b65cacf 100644
--- a/program/shinyApp/R/enrichment_analysis/overrepresentation_analysis.R
+++ b/program/shinyApp/R/enrichment_analysis/overrepresentation_analysis.R
@@ -67,37 +67,37 @@ over_representation_analysis <- function(
EnrichmentRes_C8 <- NULL
# KEGG
if(enrichments2do$KEGG){
- if(!(identical(list("Universe"=input$UniverseOfGene),par_tmp[[session_key]]$OA$KEGG ))){
+ if(!(identical(list("Universe"=input$UniverseOfGene),par_tmp[[session$token]]$OA$KEGG ))){
EnrichmentRes_KEGG <- clusterProfiler::enrichKEGG(
gene = geneSetChoice,
organism = input$OrganismChoice,
pvalueCutoff = 0.05,
universe = universeSelected_tranlsated
)
- res_tmp[[session_key]]$OA$KEGG <<- EnrichmentRes_KEGG
- par_tmp[[session_key]]$OA$KEGG <<- list("Universe"=input$UniverseOfGene)
+ res_tmp[[session$token]]$OA$KEGG <<- EnrichmentRes_KEGG
+ par_tmp[[session$token]]$OA$KEGG <<- list("Universe"=input$UniverseOfGene)
}else{
- EnrichmentRes_KEGG <- res_tmp[[session_key]]$OA$KEGG
+ EnrichmentRes_KEGG <- res_tmp[[session$token]]$OA$KEGG
}
}
# GO
if(enrichments2do$GO){
- if(!(identical(list("Universe"=input$UniverseOfGene),par_tmp[[session_key]]$OA$GO ))){
+ if(!(identical(list("Universe"=input$UniverseOfGene),par_tmp[[session$token]]$OA$GO ))){
EnrichmentRes_GO <- clusterProfiler::enrichGO(
gene = geneSetChoice,
ont = input$ontologyForGO,
pvalueCutoff = 0.05,
OrgDb = ifelse(input$OrganismChoice == "hsa","org.Hs.eg.db","org.Mm.eg.db")
)
- res_tmp[[session_key]]$OA$GO <<- EnrichmentRes_GO
- par_tmp[[session_key]]$OA$GO <<- list("Universe"=input$UniverseOfGene)
+ res_tmp[[session$token]]$OA$GO <<- EnrichmentRes_GO
+ par_tmp[[session$token]]$OA$GO <<- list("Universe"=input$UniverseOfGene)
}else{
- EnrichmentRes_GO <- res_tmp[[session_key]]$OA$GO
+ EnrichmentRes_GO <- res_tmp[[session$token]]$OA$GO
}
}
# Reactome
if(enrichments2do$REACTOME){
- if(!(identical(list("Universe"=input$UniverseOfGene),par_tmp[[session_key]]$OA$REACTOME ))){
+ if(!(identical(list("Universe"=input$UniverseOfGene),par_tmp[[session$token]]$OA$REACTOME ))){
EnrichmentRes_REACTOME <- ReactomePA::enrichPathway(
gene = geneSetChoice,
pvalueCutoff = 0.05,
@@ -105,15 +105,15 @@ over_representation_analysis <- function(
universe = universeSelected_tranlsated,
readable = T
)
- res_tmp[[session_key]]$OA$REACTOME <<- EnrichmentRes_REACTOME
- par_tmp[[session_key]]$OA$REACTOME <<- list("Universe"=input$UniverseOfGene)
+ res_tmp[[session$token]]$OA$REACTOME <<- EnrichmentRes_REACTOME
+ par_tmp[[session$token]]$OA$REACTOME <<- list("Universe"=input$UniverseOfGene)
}else{
- EnrichmentRes_REACTOME <- res_tmp[[session_key]]$OA$REACTOME
+ EnrichmentRes_REACTOME <- res_tmp[[session$token]]$OA$REACTOME
}
}
# Hallmarks
if(enrichments2do$Hallmarks){
- if(!(identical(list("Universe"=input$UniverseOfGene),par_tmp[[session_key]]$OA$Hallmarks ))){
+ if(!(identical(list("Universe"=input$UniverseOfGene),par_tmp[[session$token]]$OA$Hallmarks ))){
Hallmarkset <- msigdbr(
species = ifelse(input$OrganismChoice == "hsa","Homo sapiens","Mus musculus"),
category = "H",
@@ -125,15 +125,15 @@ over_representation_analysis <- function(
universe = universeSelected_tranlsated,
TERM2GENE = Hallmarkset
)
- res_tmp[[session_key]]$OA$Hallmarks <<- EnrichmentRes_Hallmarks
- par_tmp[[session_key]]$OA$Hallmarks <<- list("Universe"=input$UniverseOfGene)
+ res_tmp[[session$token]]$OA$Hallmarks <<- EnrichmentRes_Hallmarks
+ par_tmp[[session$token]]$OA$Hallmarks <<- list("Universe"=input$UniverseOfGene)
}else{
- EnrichmentRes_Hallmarks <- res_tmp[[session_key]]$OA$Hallmarks
+ EnrichmentRes_Hallmarks <- res_tmp[[session$token]]$OA$Hallmarks
}
}
# C1
if(enrichments2do$C1){
- if(!(identical(list("Universe"=input$UniverseOfGene),par_tmp[[session_key]]$OA$C1 ))){
+ if(!(identical(list("Universe"=input$UniverseOfGene),par_tmp[[session$token]]$OA$C1 ))){
C1set <- msigdbr(
species = ifelse(input$OrganismChoice == "hsa","Homo sapiens","Mus musculus"),
category = "C1",
@@ -145,15 +145,15 @@ over_representation_analysis <- function(
universe = universeSelected_tranlsated,
TERM2GENE = C1set
)
- res_tmp[[session_key]]$OA$C1 <<- EnrichmentRes_C1
- par_tmp[[session_key]]$OA$C1 <<- list("Universe"=input$UniverseOfGene)
+ res_tmp[[session$token]]$OA$C1 <<- EnrichmentRes_C1
+ par_tmp[[session$token]]$OA$C1 <<- list("Universe"=input$UniverseOfGene)
}else{
- EnrichmentRes_C1 <- res_tmp[[session_key]]$OA$C1
+ EnrichmentRes_C1 <- res_tmp[[session$token]]$OA$C1
}
}
# C2
if(enrichments2do$C2){
- if(!(identical(list("Universe"=input$UniverseOfGene),par_tmp[[session_key]]$OA$C2 ))){
+ if(!(identical(list("Universe"=input$UniverseOfGene),par_tmp[[session$token]]$OA$C2 ))){
C2set <- msigdbr(
species = ifelse(input$OrganismChoice == "hsa","Homo sapiens","Mus musculus"),
category = "C2",
@@ -165,15 +165,15 @@ over_representation_analysis <- function(
universe = universeSelected_tranlsated,
TERM2GENE = C2set
)
- res_tmp[[session_key]]$OA$C2 <<- EnrichmentRes_C2
- par_tmp[[session_key]]$OA$C2 <<- list("Universe"=input$UniverseOfGene)
+ res_tmp[[session$token]]$OA$C2 <<- EnrichmentRes_C2
+ par_tmp[[session$token]]$OA$C2 <<- list("Universe"=input$UniverseOfGene)
}else{
- EnrichmentRes_C2 <- res_tmp[[session_key]]$OA$C2
+ EnrichmentRes_C2 <- res_tmp[[session$token]]$OA$C2
}
}
# C3
if(enrichments2do$C3){
- if(!(identical(list("Universe"=input$UniverseOfGene),par_tmp[[session_key]]$OA$C3 ))){
+ if(!(identical(list("Universe"=input$UniverseOfGene),par_tmp[[session$token]]$OA$C3 ))){
C3set <- msigdbr(
species = ifelse(input$OrganismChoice == "hsa","Homo sapiens","Mus musculus"),
category = "C3",
@@ -185,15 +185,15 @@ over_representation_analysis <- function(
universe = universeSelected_tranlsated,
TERM2GENE = C3set
)
- res_tmp[[session_key]]$OA$C3 <<- EnrichmentRes_C3
- par_tmp[[session_key]]$OA$C3 <<- list("Universe"=input$UniverseOfGene)
+ res_tmp[[session$token]]$OA$C3 <<- EnrichmentRes_C3
+ par_tmp[[session$token]]$OA$C3 <<- list("Universe"=input$UniverseOfGene)
}else{
- EnrichmentRes_C3 <- res_tmp[[session_key]]$OA$C3
+ EnrichmentRes_C3 <- res_tmp[[session$token]]$OA$C3
}
}
# C4
if(enrichments2do$C4){
- if(!(identical(list("Universe"=input$UniverseOfGene),par_tmp[[session_key]]$OA$C4 ))){
+ if(!(identical(list("Universe"=input$UniverseOfGene),par_tmp[[session$token]]$OA$C4 ))){
C4set <- msigdbr(
species = ifelse(input$OrganismChoice == "hsa","Homo sapiens","Mus musculus"),
category = "C4",
@@ -205,15 +205,15 @@ over_representation_analysis <- function(
universe = universeSelected_tranlsated,
TERM2GENE = C4set
)
- res_tmp[[session_key]]$OA$C4 <<- EnrichmentRes_C4
- par_tmp[[session_key]]$OA$C4 <<- list("Universe"=input$UniverseOfGene)
+ res_tmp[[session$token]]$OA$C4 <<- EnrichmentRes_C4
+ par_tmp[[session$token]]$OA$C4 <<- list("Universe"=input$UniverseOfGene)
}else{
- EnrichmentRes_C4 <- res_tmp[[session_key]]$OA$C4
+ EnrichmentRes_C4 <- res_tmp[[session$token]]$OA$C4
}
}
# C5
if(enrichments2do$C5){
- if(!(identical(list("Universe"=input$UniverseOfGene),par_tmp[[session_key]]$OA$C5 ))){
+ if(!(identical(list("Universe"=input$UniverseOfGene),par_tmp[[session$token]]$OA$C5 ))){
C5set <- msigdbr(
species = ifelse(input$OrganismChoice == "hsa","Homo sapiens","Mus musculus"),
category = "C5",
@@ -225,15 +225,15 @@ over_representation_analysis <- function(
universe = universeSelected_tranlsated,
TERM2GENE = C5set
)
- res_tmp[[session_key]]$OA$C5 <<- EnrichmentRes_C5
- par_tmp[[session_key]]$OA$C5 <<- list("Universe"=input$UniverseOfGene)
+ res_tmp[[session$token]]$OA$C5 <<- EnrichmentRes_C5
+ par_tmp[[session$token]]$OA$C5 <<- list("Universe"=input$UniverseOfGene)
}else{
- EnrichmentRes_C5 <- res_tmp[[session_key]]$OA$C5
+ EnrichmentRes_C5 <- res_tmp[[session$token]]$OA$C5
}
}
# C6
if(enrichments2do$C6){
- if(!(identical(list("Universe"=input$UniverseOfGene),par_tmp[[session_key]]$OA$C6 ))){
+ if(!(identical(list("Universe"=input$UniverseOfGene),par_tmp[[session$token]]$OA$C6 ))){
C6set <- msigdbr(
species = ifelse(input$OrganismChoice == "hsa","Homo sapiens","Mus musculus"),
category = "C6",
@@ -245,15 +245,15 @@ over_representation_analysis <- function(
universe = universeSelected_tranlsated,
TERM2GENE = C6set
)
- res_tmp[[session_key]]$OA$C6 <<- EnrichmentRes_C6
- par_tmp[[session_key]]$OA$C6 <<- list("Universe"=input$UniverseOfGene)
+ res_tmp[[session$token]]$OA$C6 <<- EnrichmentRes_C6
+ par_tmp[[session$token]]$OA$C6 <<- list("Universe"=input$UniverseOfGene)
}else{
- EnrichmentRes_C6 <- res_tmp[[session_key]]$OA$C6
+ EnrichmentRes_C6 <- res_tmp[[session$token]]$OA$C6
}
}
# C7 ImmuneSigDB subset
if(enrichments2do$C7){
- if(!(identical(list("Universe"=input$UniverseOfGene),par_tmp[[session_key]]$OA$C7 ))){
+ if(!(identical(list("Universe"=input$UniverseOfGene),par_tmp[[session$token]]$OA$C7 ))){
C7set <- msigdbr(
species = ifelse(input$OrganismChoice == "hsa","Homo sapiens","Mus musculus"),
category = "C7",
@@ -266,15 +266,15 @@ over_representation_analysis <- function(
universe = universeSelected_tranlsated,
TERM2GENE = C7set
)
- res_tmp[[session_key]]$OA$C7 <<- EnrichmentRes_C7
- par_tmp[[session_key]]$OA$C7 <<- list("Universe"=input$UniverseOfGene)
+ res_tmp[[session$token]]$OA$C7 <<- EnrichmentRes_C7
+ par_tmp[[session$token]]$OA$C7 <<- list("Universe"=input$UniverseOfGene)
}else{
- EnrichmentRes_C7 <- res_tmp[[session_key]]$OA$C7
+ EnrichmentRes_C7 <- res_tmp[[session$token]]$OA$C7
}
}
# C8
if(enrichments2do$C8){
- if(!(identical(list("Universe"=input$UniverseOfGene),par_tmp[[session_key]]$OA$C8 ))){
+ if(!(identical(list("Universe"=input$UniverseOfGene),par_tmp[[session$token]]$OA$C8 ))){
C8set <- msigdbr(
species = ifelse(input$OrganismChoice == "hsa","Homo sapiens","Mus musculus"),
category = "C8",
@@ -286,15 +286,15 @@ over_representation_analysis <- function(
universe = universeSelected_tranlsated,
TERM2GENE = C8set
)
- res_tmp[[session_key]]$OA$C8 <<- EnrichmentRes_C8
- par_tmp[[session_key]]$OA$C8 <<- list("Universe"=input$UniverseOfGene)
+ res_tmp[[session$token]]$OA$C8 <<- EnrichmentRes_C8
+ par_tmp[[session$token]]$OA$C8 <<- list("Universe"=input$UniverseOfGene)
}else{
- EnrichmentRes_C8 <- res_tmp[[session_key]]$OA$C8
+ EnrichmentRes_C8 <- res_tmp[[session$token]]$OA$C8
}
}
# C2 subset CGP
if(enrichments2do$CGP){
- if(!(identical(list("Universe"=input$UniverseOfGene),par_tmp[[session_key]]$OA$CGP ))){
+ if(!(identical(list("Universe"=input$UniverseOfGene),par_tmp[[session$token]]$OA$CGP ))){
genesets4ea <- msigdbr(
species = ifelse(input$OrganismChoice == "hsa","Homo sapiens","Mus musculus"),
category = "C2",
@@ -307,15 +307,15 @@ over_representation_analysis <- function(
universe = universeSelected_tranlsated,
TERM2GENE = genesets4ea
)
- res_tmp[[session_key]]$OA$CGP <<- EnrichmentRes_CGP
- par_tmp[[session_key]]$OA$CGP <<- list("Universe"=input$UniverseOfGene)
+ res_tmp[[session$token]]$OA$CGP <<- EnrichmentRes_CGP
+ par_tmp[[session$token]]$OA$CGP <<- list("Universe"=input$UniverseOfGene)
}else{
- EnrichmentRes_CGP <- res_tmp[[session_key]]$OA$CGP
+ EnrichmentRes_CGP <- res_tmp[[session$token]]$OA$CGP
}
}
# C2 subset CP
if(enrichments2do$CP){
- if(!(identical(list("Universe"=input$UniverseOfGene),par_tmp[[session_key]]$OA$CP ))){
+ if(!(identical(list("Universe"=input$UniverseOfGene),par_tmp[[session$token]]$OA$CP ))){
genesets4ea <- msigdbr(
species = ifelse(input$OrganismChoice == "hsa","Homo sapiens","Mus musculus"),
category = "C2",
@@ -328,15 +328,15 @@ over_representation_analysis <- function(
universe = universeSelected_tranlsated,
TERM2GENE = genesets4ea
)
- res_tmp[[session_key]]$OA$CP <<- EnrichmentRes_CP
- par_tmp[[session_key]]$OA$CP <<- list("Universe"=input$UniverseOfGene)
+ res_tmp[[session$token]]$OA$CP <<- EnrichmentRes_CP
+ par_tmp[[session$token]]$OA$CP <<- list("Universe"=input$UniverseOfGene)
}else{
- EnrichmentRes_CP <- res_tmp[[session_key]]$OA$CP
+ EnrichmentRes_CP <- res_tmp[[session$token]]$OA$CP
}
}
# C2:CP subset BIOCARTA
if(enrichments2do$BIOCARTA){
- if(!(identical(list("Universe"=input$UniverseOfGene),par_tmp[[session_key]]$OA$BIOCARTA ))){
+ if(!(identical(list("Universe"=input$UniverseOfGene),par_tmp[[session$token]]$OA$BIOCARTA ))){
genesets4ea <- msigdbr(
species = ifelse(input$OrganismChoice == "hsa","Homo sapiens","Mus musculus"),
category = "C2",
@@ -349,15 +349,15 @@ over_representation_analysis <- function(
universe = universeSelected_tranlsated,
TERM2GENE = genesets4ea
)
- res_tmp[[session_key]]$OA$BIOCARTA <<- EnrichmentRes_BIOCARTA
- par_tmp[[session_key]]$OA$BIOCARTA <<- list("Universe"=input$UniverseOfGene)
+ res_tmp[[session$token]]$OA$BIOCARTA <<- EnrichmentRes_BIOCARTA
+ par_tmp[[session$token]]$OA$BIOCARTA <<- list("Universe"=input$UniverseOfGene)
}else{
- EnrichmentRes_BIOCARTA <- res_tmp[[session_key]]$OA$BIOCARTA
+ EnrichmentRes_BIOCARTA <- res_tmp[[session$token]]$OA$BIOCARTA
}
}
# C2:CP subset PID
if(enrichments2do$PID){
- if(!(identical(list("Universe"=input$UniverseOfGene),par_tmp[[session_key]]$OA$PID ))){
+ if(!(identical(list("Universe"=input$UniverseOfGene),par_tmp[[session$token]]$OA$PID ))){
genesets4ea <- msigdbr(
species = ifelse(input$OrganismChoice == "hsa","Homo sapiens","Mus musculus"),
category = "C2",
@@ -370,15 +370,15 @@ over_representation_analysis <- function(
universe = universeSelected_tranlsated,
TERM2GENE = genesets4ea
)
- res_tmp[[session_key]]$OA$PID <<- EnrichmentRes_PID
- par_tmp[[session_key]]$OA$PID <<- list("Universe"=input$UniverseOfGene)
+ res_tmp[[session$token]]$OA$PID <<- EnrichmentRes_PID
+ par_tmp[[session$token]]$OA$PID <<- list("Universe"=input$UniverseOfGene)
}else{
- EnrichmentRes_PID <- res_tmp[[session_key]]$OA$PID
+ EnrichmentRes_PID <- res_tmp[[session$token]]$OA$PID
}
}
# C2:CP subset REACTOME
if(enrichments2do$REACTOME){
- if(!(identical(list("Universe"=input$UniverseOfGene),par_tmp[[session_key]]$OA$REACTOME ))){
+ if(!(identical(list("Universe"=input$UniverseOfGene),par_tmp[[session$token]]$OA$REACTOME ))){
genesets4ea <- msigdbr(
species = ifelse(input$OrganismChoice == "hsa","Homo sapiens","Mus musculus"),
category = "C2",
@@ -391,15 +391,15 @@ over_representation_analysis <- function(
universe = universeSelected_tranlsated,
TERM2GENE = genesets4ea
)
- res_tmp[[session_key]]$OA$REACTOME <<- EnrichmentRes_REACTOME
- par_tmp[[session_key]]$OA$REACTOME <<- list("Universe"=input$UniverseOfGene)
+ res_tmp[[session$token]]$OA$REACTOME <<- EnrichmentRes_REACTOME
+ par_tmp[[session$token]]$OA$REACTOME <<- list("Universe"=input$UniverseOfGene)
}else{
- EnrichmentRes_REACTOME <- res_tmp[[session_key]]$OA$REACTOME
+ EnrichmentRes_REACTOME <- res_tmp[[session$token]]$OA$REACTOME
}
}
# C2:CP subset WIKIPATHWAYS
if(enrichments2do$WIKIPATHWAYS){
- if(!(identical(list("Universe"=input$UniverseOfGene),par_tmp[[session_key]]$OA$WIKIPATHWAYS ))){
+ if(!(identical(list("Universe"=input$UniverseOfGene),par_tmp[[session$token]]$OA$WIKIPATHWAYS ))){
genesets4ea <- msigdbr(
species = ifelse(input$OrganismChoice == "hsa","Homo sapiens","Mus musculus"),
category = "C2",
@@ -412,15 +412,15 @@ over_representation_analysis <- function(
universe = universeSelected_tranlsated,
TERM2GENE = genesets4ea
)
- res_tmp[[session_key]]$OA$WIKIPATHWAYS <<- EnrichmentRes_WIKIPATHWAYS
- par_tmp[[session_key]]$OA$WIKIPATHWAYS <<- list("Universe"=input$UniverseOfGene)
+ res_tmp[[session$token]]$OA$WIKIPATHWAYS <<- EnrichmentRes_WIKIPATHWAYS
+ par_tmp[[session$token]]$OA$WIKIPATHWAYS <<- list("Universe"=input$UniverseOfGene)
}else{
- EnrichmentRes_WIKIPATHWAYS <- res_tmp[[session_key]]$OA$WIKIPATHWAYS
+ EnrichmentRes_WIKIPATHWAYS <- res_tmp[[session$token]]$OA$WIKIPATHWAYS
}
}
# C3 subset MIR:MIRDB
if(enrichments2do$MIRDB){
- if(!(identical(list("Universe"=input$UniverseOfGene),par_tmp[[session_key]]$OA$MIRDB ))){
+ if(!(identical(list("Universe"=input$UniverseOfGene),par_tmp[[session$token]]$OA$MIRDB ))){
genesets4ea <- msigdbr(
species = ifelse(input$OrganismChoice == "hsa","Homo sapiens","Mus musculus"),
category = "C3",
@@ -433,15 +433,15 @@ over_representation_analysis <- function(
universe = universeSelected_tranlsated,
TERM2GENE = genesets4ea
)
- res_tmp[[session_key]]$OA$MIRDB <<- EnrichmentRes_MIRDB
- par_tmp[[session_key]]$OA$MIRDB <<- list("Universe"=input$UniverseOfGene)
+ res_tmp[[session$token]]$OA$MIRDB <<- EnrichmentRes_MIRDB
+ par_tmp[[session$token]]$OA$MIRDB <<- list("Universe"=input$UniverseOfGene)
}else{
- EnrichmentRes_MIRDB <- res_tmp[[session_key]]$OA$MIRDB
+ EnrichmentRes_MIRDB <- res_tmp[[session$token]]$OA$MIRDB
}
}
# C3 subset MIR:MIR_Legacy
if(enrichments2do$MIR_Legacy){
- if(!(identical(list("Universe"=input$UniverseOfGene),par_tmp[[session_key]]$OA$MIR_Legacy ))){
+ if(!(identical(list("Universe"=input$UniverseOfGene),par_tmp[[session$token]]$OA$MIR_Legacy ))){
genesets4ea <- msigdbr(
species = ifelse(input$OrganismChoice == "hsa","Homo sapiens","Mus musculus"),
category = "C3",
@@ -454,15 +454,15 @@ over_representation_analysis <- function(
universe = universeSelected_tranlsated,
TERM2GENE = genesets4ea
)
- res_tmp[[session_key]]$OA$MIR_Legacy <<- EnrichmentRes_MIR_Legacy
- par_tmp[[session_key]]$OA$MIR_Legacy <<- list("Universe"=input$UniverseOfGene)
+ res_tmp[[session$token]]$OA$MIR_Legacy <<- EnrichmentRes_MIR_Legacy
+ par_tmp[[session$token]]$OA$MIR_Legacy <<- list("Universe"=input$UniverseOfGene)
}else{
- EnrichmentRes_MIR_Legacy <- res_tmp[[session_key]]$OA$MIR_Legacy
+ EnrichmentRes_MIR_Legacy <- res_tmp[[session$token]]$OA$MIR_Legacy
}
}
# C3 subset TFT:GTRD
if(enrichments2do$GTRD){
- if(!(identical(list("Universe"=input$UniverseOfGene),par_tmp[[session_key]]$OA$GTRD ))){
+ if(!(identical(list("Universe"=input$UniverseOfGene),par_tmp[[session$token]]$OA$GTRD ))){
genesets4ea <- msigdbr(
species = ifelse(input$OrganismChoice == "hsa","Homo sapiens","Mus musculus"),
category = "C3",
@@ -475,15 +475,15 @@ over_representation_analysis <- function(
universe = universeSelected_tranlsated,
TERM2GENE = genesets4ea
)
- res_tmp[[session_key]]$OA$GTRD <<- EnrichmentRes_GTRD
- par_tmp[[session_key]]$OA$GTRD <<- list("Universe"=input$UniverseOfGene)
+ res_tmp[[session$token]]$OA$GTRD <<- EnrichmentRes_GTRD
+ par_tmp[[session$token]]$OA$GTRD <<- list("Universe"=input$UniverseOfGene)
}else{
- EnrichmentRes_GTRD <- res_tmp[[session_key]]$OA$GTRD
+ EnrichmentRes_GTRD <- res_tmp[[session$token]]$OA$GTRD
}
}
# C3 subset TFT:TFT_Legacy
if(enrichments2do$TFT_Legacy){
- if(!(identical(list("Universe"=input$UniverseOfGene),par_tmp[[session_key]]$OA$TFT_Legacy ))){
+ if(!(identical(list("Universe"=input$UniverseOfGene),par_tmp[[session$token]]$OA$TFT_Legacy ))){
genesets4ea <- msigdbr(
species = ifelse(input$OrganismChoice == "hsa","Homo sapiens","Mus musculus"),
category = "C3",
@@ -496,15 +496,15 @@ over_representation_analysis <- function(
universe = universeSelected_tranlsated,
TERM2GENE = genesets4ea
)
- res_tmp[[session_key]]$OA$TFT_Legacy <<- EnrichmentRes_TFT_Legacy
- par_tmp[[session_key]]$OA$TFT_Legacy <<- list("Universe"=input$UniverseOfGene)
+ res_tmp[[session$token]]$OA$TFT_Legacy <<- EnrichmentRes_TFT_Legacy
+ par_tmp[[session$token]]$OA$TFT_Legacy <<- list("Universe"=input$UniverseOfGene)
}else{
- EnrichmentRes_TFT_Legacy <- res_tmp[[session_key]]$OA$TFT_Legacy
+ EnrichmentRes_TFT_Legacy <- res_tmp[[session$token]]$OA$TFT_Legacy
}
}
# C4 subset CGN
if(enrichments2do$CGN){
- if(!(identical(list("Universe"=input$UniverseOfGene),par_tmp[[session_key]]$OA$CGN ))){
+ if(!(identical(list("Universe"=input$UniverseOfGene),par_tmp[[session$token]]$OA$CGN ))){
genesets4ea <- msigdbr(
species = ifelse(input$OrganismChoice == "hsa","Homo sapiens","Mus musculus"),
category = "C4",
@@ -517,15 +517,15 @@ over_representation_analysis <- function(
universe = universeSelected_tranlsated,
TERM2GENE = genesets4ea
)
- res_tmp[[session_key]]$OA$CGN <<- EnrichmentRes_CGN
- par_tmp[[session_key]]$OA$CGN <<- list("Universe"=input$UniverseOfGene)
+ res_tmp[[session$token]]$OA$CGN <<- EnrichmentRes_CGN
+ par_tmp[[session$token]]$OA$CGN <<- list("Universe"=input$UniverseOfGene)
}else{
- EnrichmentRes_CGN <- res_tmp[[session_key]]$OA$CGN
+ EnrichmentRes_CGN <- res_tmp[[session$token]]$OA$CGN
}
}
# C4 subset CM
if(enrichments2do$CM){
- if(!(identical(list("Universe"=input$UniverseOfGene),par_tmp[[session_key]]$OA$CM ))){
+ if(!(identical(list("Universe"=input$UniverseOfGene),par_tmp[[session$token]]$OA$CM ))){
genesets4ea <- msigdbr(
species = ifelse(input$OrganismChoice == "hsa","Homo sapiens","Mus musculus"),
category = "C4",
@@ -538,15 +538,15 @@ over_representation_analysis <- function(
universe = universeSelected_tranlsated,
TERM2GENE = genesets4ea
)
- res_tmp[[session_key]]$OA$CM <<- EnrichmentRes_CM
- par_tmp[[session_key]]$OA$CM <<- list("Universe"=input$UniverseOfGene)
+ res_tmp[[session$token]]$OA$CM <<- EnrichmentRes_CM
+ par_tmp[[session$token]]$OA$CM <<- list("Universe"=input$UniverseOfGene)
}else{
- EnrichmentRes_CM <- res_tmp[[session_key]]$OA$CM
+ EnrichmentRes_CM <- res_tmp[[session$token]]$OA$CM
}
}
# C5 subset GO BP
if(enrichments2do$GO_BP){
- if(!(identical(list("Universe"=input$UniverseOfGene),par_tmp[[session_key]]$OA$GO_BP ))){
+ if(!(identical(list("Universe"=input$UniverseOfGene),par_tmp[[session$token]]$OA$GO_BP ))){
genesets4ea <- msigdbr(
species = ifelse(input$OrganismChoice == "hsa","Homo sapiens","Mus musculus"),
category = "C5",
@@ -559,15 +559,15 @@ over_representation_analysis <- function(
universe = universeSelected_tranlsated,
TERM2GENE = genesets4ea
)
- res_tmp[[session_key]]$OA$GO_BP <<- EnrichmentRes_GO_BP
- par_tmp[[session_key]]$OA$GO_BP <<- list("Universe"=input$UniverseOfGene)
+ res_tmp[[session$token]]$OA$GO_BP <<- EnrichmentRes_GO_BP
+ par_tmp[[session$token]]$OA$GO_BP <<- list("Universe"=input$UniverseOfGene)
}else{
- EnrichmentRes_GO_BP <- res_tmp[[session_key]]$OA$GO_BP
+ EnrichmentRes_GO_BP <- res_tmp[[session$token]]$OA$GO_BP
}
}
# C5 subset GO CC
if(enrichments2do$GO_CC){
- if(!(identical(list("Universe"=input$UniverseOfGene),par_tmp[[session_key]]$OA$GO_CC ))){
+ if(!(identical(list("Universe"=input$UniverseOfGene),par_tmp[[session$token]]$OA$GO_CC ))){
genesets4ea <- msigdbr(
species = ifelse(input$OrganismChoice == "hsa","Homo sapiens","Mus musculus"),
category = "C5",
@@ -580,15 +580,15 @@ over_representation_analysis <- function(
universe = universeSelected_tranlsated,
TERM2GENE = genesets4ea
)
- res_tmp[[session_key]]$OA$GO_CC <<- EnrichmentRes_GO_CC
- par_tmp[[session_key]]$OA$GO_CC <<- list("Universe"=input$UniverseOfGene)
+ res_tmp[[session$token]]$OA$GO_CC <<- EnrichmentRes_GO_CC
+ par_tmp[[session$token]]$OA$GO_CC <<- list("Universe"=input$UniverseOfGene)
}else{
- EnrichmentRes_GO_CC <- res_tmp[[session_key]]$OA$GO_CC
+ EnrichmentRes_GO_CC <- res_tmp[[session$token]]$OA$GO_CC
}
}
# C5 subset GO MF
if(enrichments2do$GO_MF){
- if(!(identical(list("Universe"=input$UniverseOfGene),par_tmp[[session_key]]$OA$GO_MF ))){
+ if(!(identical(list("Universe"=input$UniverseOfGene),par_tmp[[session$token]]$OA$GO_MF ))){
genesets4ea <- msigdbr(
species = ifelse(input$OrganismChoice == "hsa","Homo sapiens","Mus musculus"),
category = "C5",
@@ -601,15 +601,15 @@ over_representation_analysis <- function(
universe = universeSelected_tranlsated,
TERM2GENE = genesets4ea
)
- res_tmp[[session_key]]$OA$GO_MF <<- EnrichmentRes_GO_MF
- par_tmp[[session_key]]$OA$GO_MF <<- list("Universe"=input$UniverseOfGene)
+ res_tmp[[session$token]]$OA$GO_MF <<- EnrichmentRes_GO_MF
+ par_tmp[[session$token]]$OA$GO_MF <<- list("Universe"=input$UniverseOfGene)
}else{
- EnrichmentRes_GO_MF <- res_tmp[[session_key]]$OA$GO_MF
+ EnrichmentRes_GO_MF <- res_tmp[[session$token]]$OA$GO_MF
}
}
# C5 subset HPO
if(enrichments2do$HPO){
- if(!(identical(list("Universe"=input$UniverseOfGene),par_tmp[[session_key]]$OA$HPO ))){
+ if(!(identical(list("Universe"=input$UniverseOfGene),par_tmp[[session$token]]$OA$HPO ))){
genesets4ea <- msigdbr(
species = ifelse(input$OrganismChoice == "hsa","Homo sapiens","Mus musculus"),
category = "C5",
@@ -622,15 +622,15 @@ over_representation_analysis <- function(
universe = universeSelected_tranlsated,
TERM2GENE = genesets4ea
)
- res_tmp[[session_key]]$OA$HPO <<- EnrichmentRes_HPO
- par_tmp[[session_key]]$OA$HPO <<- list("Universe"=input$UniverseOfGene)
+ res_tmp[[session$token]]$OA$HPO <<- EnrichmentRes_HPO
+ par_tmp[[session$token]]$OA$HPO <<- list("Universe"=input$UniverseOfGene)
}else{
- EnrichmentRes_HPO <- res_tmp[[session_key]]$OA$HPO
+ EnrichmentRes_HPO <- res_tmp[[session$token]]$OA$HPO
}
}
# C7 subset IMMUNESIGDB
if(enrichments2do$IMMUNESIGDB){
- if(!(identical(list("Universe"=input$UniverseOfGene),par_tmp[[session_key]]$OA$IMMUNESIGDB ))){
+ if(!(identical(list("Universe"=input$UniverseOfGene),par_tmp[[session$token]]$OA$IMMUNESIGDB ))){
genesets4ea <- msigdbr(
species = ifelse(input$OrganismChoice == "hsa","Homo sapiens","Mus musculus"),
category = "C7",
@@ -643,15 +643,15 @@ over_representation_analysis <- function(
universe = universeSelected_tranlsated,
TERM2GENE = genesets4ea
)
- res_tmp[[session_key]]$OA$IMMUNESIGDB <<- EnrichmentRes_IMMUNESIGDB
- par_tmp[[session_key]]$OA$IMMUNESIGDB <<- list("Universe"=input$UniverseOfGene)
+ res_tmp[[session$token]]$OA$IMMUNESIGDB <<- EnrichmentRes_IMMUNESIGDB
+ par_tmp[[session$token]]$OA$IMMUNESIGDB <<- list("Universe"=input$UniverseOfGene)
}else{
- EnrichmentRes_IMMUNESIGDB <- res_tmp[[session_key]]$OA$IMMUNESIGDB
+ EnrichmentRes_IMMUNESIGDB <- res_tmp[[session$token]]$OA$IMMUNESIGDB
}
}
# C7 subset VAX
if(enrichments2do$VAX){
- if(!(identical(list("Universe"=input$UniverseOfGene),par_tmp[[session_key]]$OA$VAX ))){
+ if(!(identical(list("Universe"=input$UniverseOfGene),par_tmp[[session$token]]$OA$VAX ))){
genesets4ea <- msigdbr(
species = ifelse(input$OrganismChoice == "hsa","Homo sapiens","Mus musculus"),
category = "C7",
@@ -664,10 +664,10 @@ over_representation_analysis <- function(
universe = universeSelected_tranlsated,
TERM2GENE = genesets4ea
)
- res_tmp[[session_key]]$OA$VAX <<- EnrichmentRes_VAX
- par_tmp[[session_key]]$OA$VAX <<- list("Universe"=input$UniverseOfGene)
+ res_tmp[[session$token]]$OA$VAX <<- EnrichmentRes_VAX
+ par_tmp[[session$token]]$OA$VAX <<- list("Universe"=input$UniverseOfGene)
}else{
- EnrichmentRes_VAX <- res_tmp[[session_key]]$OA$VAX
+ EnrichmentRes_VAX <- res_tmp[[session$token]]$OA$VAX
}
}
diff --git a/program/shinyApp/R/enrichment_analysis/server.R b/program/shinyApp/R/enrichment_analysis/server.R
index bc91fa91..c57e2c35 100644
--- a/program/shinyApp/R/enrichment_analysis/server.R
+++ b/program/shinyApp/R/enrichment_analysis/server.R
@@ -791,9 +791,9 @@ enrichment_analysis_Server <- function(id, data, params, updates){
}
ea_reactives$ea_info <- "**Enrichment Analysis Done!**"
# res_temp Zuweisung
- res_tmp[[session_key]]["Enrichment"] <<- ea_reactives$enrichment_results
+ res_tmp[[session$token]]["Enrichment"] <<- ea_reactives$enrichment_results
# par_temp Zuweisung
- par_tmp[[session_key]]["Enrichment"] <<- list(
+ par_tmp[[session$token]]["Enrichment"] <<- list(
"ValueToAttach" = input$ValueToAttach,
"GeneSet2Enrich" = input$GeneSet2Enrich,
"Groups2Compare_ref_GSEA" = input$Groups2Compare_ref_GSEA,
diff --git a/program/shinyApp/R/heatmap/server.R b/program/shinyApp/R/heatmap/server.R
index c13816ce..2f43a592 100644
--- a/program/shinyApp/R/heatmap/server.R
+++ b/program/shinyApp/R/heatmap/server.R
@@ -219,10 +219,9 @@ heatmap_server <- function(id, data, params, updates){
input$anno_options,
input$row_label_options
)
- browser()
req(selectedData_processed())
# update the data if needed
- data <- update_data(data, session_key)
+ data <- update_data(session$token)
heatmap_reactives$current_updates <- updates()
print("Heatmap on selected Data")
# Value need to be setted in case there is nothing to plot to avoid crash
@@ -363,7 +362,6 @@ heatmap_server <- function(id, data, params, updates){
}
if(calculate == 1){
if(input$LFC_toHeatmap){
- browser()
ctrl_samples_idx <- which(
colData(data$data)[,input$sample_annotation_types_cmp_heatmap]%in%input$Groups2Compare_ref_heatmap
)
@@ -375,7 +373,7 @@ heatmap_server <- function(id, data, params, updates){
output$Options_selected_out_3 <- renderText("Choose variable with at least two samples per condition!")
doThis_flag <- F
}
- if(par_tmp[[session_key]]$PreProcessing_Procedure == "simpleCenterScaling"|
+ if(par_tmp[[session$token]]$PreProcessing_Procedure == "simpleCenterScaling"|
any(assay(data$data))< 0){
print("Remember do not use normal center + scaling (negative Values!)")
@@ -456,15 +454,15 @@ heatmap_server <- function(id, data, params, updates){
} else {
print("Plotting saved result")
if(input$LFC_toHeatmap){
- myBreaks <- c(seq(min(res_tmp[[session_key]]$Heatmap$LFC), 0, length.out=ceiling(paletteLength/2) + 1),
- seq(max(res_tmp[[session_key]]$Heatmap$LFC)/paletteLength, max(res_tmp[[session_key]]$Heatmap$LFC), length.out=floor(paletteLength/2)))
+ myBreaks <- c(seq(min(res_tmp[[session$token]]$Heatmap$LFC), 0, length.out=ceiling(paletteLength/2) + 1),
+ seq(max(res_tmp[[session$token]]$Heatmap$LFC)/paletteLength, max(res_tmp[[session$token]]$Heatmap$LFC), length.out=floor(paletteLength/2)))
annotation_col <- rowData(data2Plot)[,input$row_anno_options,drop=F]
scenario <- 10
heatmap_plot <- pheatmap(
- t(res_tmp[[session_key]]$Heatmap[,"LFC",drop=F]),
+ t(res_tmp[[session$token]]$Heatmap[,"LFC",drop=F]),
main = gsub("^Heatmap","Heatmap_LFC",customTitleHeatmap),
- show_rownames = ifelse(nrow(res_tmp[[session_key]]$Heatmap)<=25,TRUE,FALSE),
+ show_rownames = ifelse(nrow(res_tmp[[session$token]]$Heatmap)<=25,TRUE,FALSE),
show_colnames = TRUE,
cluster_cols = input$cluster_cols,
cluster_rows = FALSE,
@@ -475,12 +473,12 @@ heatmap_server <- function(id, data, params, updates){
color = myColor_fill
)
} else {
- clusterRowspossible <- ifelse(nrow(as.matrix(res_tmp[[session_key]]$Heatmap))>1,input$cluster_rows,F)
- if(any(is.na(res_tmp[[session_key]]$Heatmap))){
- idx_of_nas <- which(apply(res_tmp[[session_key]]$Heatmap,1,is.na)) # why do we produce Nas?
+ clusterRowspossible <- ifelse(nrow(as.matrix(res_tmp[[session$token]]$Heatmap))>1,input$cluster_rows,F)
+ if(any(is.na(res_tmp[[session$token]]$Heatmap))){
+ idx_of_nas <- which(apply(res_tmp[[session$token]]$Heatmap,1,is.na)) # why do we produce Nas?
print(idx_of_nas)
if(length(idx_of_nas)>0){
- res_tmp[[session_key]]$Heatmap <- res_tmp[[session_key]]$Heatmap[-idx_of_nas,]
+ res_tmp[[session$token]]$Heatmap <- res_tmp[[session$token]]$Heatmap[-idx_of_nas,]
}
annotation_col <- colData(data$data)[-idx_of_nas,input$anno_options,drop=F]
@@ -497,9 +495,9 @@ heatmap_server <- function(id, data, params, updates){
}
scenario <- 11
heatmap_plot <- pheatmap(
- as.matrix(res_tmp[[session_key]]$Heatmap),
+ as.matrix(res_tmp[[session$token]]$Heatmap),
main = customTitleHeatmap,
- show_rownames = ifelse(nrow(res_tmp[[session_key]]$Heatmap)<=input$row_label_no,TRUE,FALSE),
+ show_rownames = ifelse(nrow(res_tmp[[session$token]]$Heatmap)<=input$row_label_no,TRUE,FALSE),
labels_row = rowData(data$data)[rownames(data2HandOver),input$row_label_options],
show_colnames = TRUE,
cluster_cols = input$cluster_cols,
@@ -534,26 +532,27 @@ heatmap_server <- function(id, data, params, updates){
# Heatmap_Groups2Compare_ctrl_heatmap <- input$Groups2Compare_ctrl_heatmap
- # res_tmp[[session_key]] gets data2HandOver or Data2Plot depending on scenario
+ # res_tmp[[session$token]] gets data2HandOver or Data2Plot depending on scenario
if(scenario == 10){
- res_tmp[[session_key]][["Heatmap"]] <<- Data2Plot
+ res_tmp[[session$token]][["Heatmap"]] <<- Data2Plot
}else if(scenario == 11){
- res_tmp[[session_key]][["Heatmap"]] <<- data2HandOver
+ res_tmp[[session$token]][["Heatmap"]] <<- data2HandOver
}
- # par_tmp[[session_key]] gets the parameters used for the heatmap
+ # par_tmp[[session$token]] gets the parameters used for the heatmap
## This exports all reactive Values in the PCA namespace
tmp <- getUserReactiveValues(input)
- par_tmp[[session_key]]$Heatmap[names(tmp)] <<- tmp
+ par_tmp[[session$token]]$Heatmap[names(tmp)] <<- tmp
output$getR_Code_Heatmap <- downloadHandler(
filename = function(){
- paste("ShinyOmics_Rcode2Reproduce_", Sys.Date(), ".zip", sep = "")
+ paste0("ShinyOmics_Rcode2Reproduce_", Sys.Date(), ".zip")
},
content = function(file){
- envList<-list(
- res_tmp[[session_key]]=res_tmp[[session_key]],
- par_tmp[[session_key]]=par_tmp[[session_key]]
+ # TODO: I think these are the completely wrong objects to save here. Needs Check!
+ envList <- list(
+ res_tmp = res_tmp[[session$token]],
+ par_tmp = par_tmp[[session$token]]
)
temp_directory <- file.path(tempdir(), as.integer(Sys.time()))
@@ -574,8 +573,8 @@ heatmap_server <- function(id, data, params, updates){
)
output$SavePlot_Heatmap <- downloadHandler(
- filename = function() {
- paste(Heatmap_customTitleHeatmap, " ",Sys.time(),input$file_ext_Heatmap,sep="")
+ filename = function() {
+ paste0(Heatmap_customTitleHeatmap, " ", Sys.time(), input$file_ext_Heatmap)
},
content = function(file){
save_pheatmap(heatmap_plot,filename=file,type=gsub("\\.","",input$file_ext_Heatmap))
@@ -583,7 +582,7 @@ heatmap_server <- function(id, data, params, updates){
tmp_filename <- paste0(
getwd(),
"/www/",
- paste(paste(Heatmap_customTitleHeatmap, " ",Sys.time(),input$file_ext_Heatmap,sep=""))
+ paste0(Heatmap_customTitleHeatmap, " ", Sys.time(), input$file_ext_Heatmap)
)
save_pheatmap(
heatmap_plot,
@@ -622,8 +621,8 @@ heatmap_server <- function(id, data, params, updates){
)
output$SaveGeneList_Heatmap <- downloadHandler(
- filename = function() {
- paste("GeneList_",customTitleHeatmap, " ",Sys.time(),".csv",sep="")
+ filename = function() {
+ paste0("GeneList_", customTitleHeatmap, " ", Sys.time(), ".csv")
},
content = function(file){
diff --git a/program/shinyApp/R/pca/server.R b/program/shinyApp/R/pca/server.R
index 71a2a68c..97365ebc 100644
--- a/program/shinyApp/R/pca/server.R
+++ b/program/shinyApp/R/pca/server.R
@@ -150,7 +150,7 @@ pca_Server <- function(id, data, params, row_select, updates){
dummy = "dummy",
sample_selection_pca = input$sample_selection_pca,
SampleAnnotationTypes_pca = input$SampleAnnotationTypes_pca
- ), "PCA", session_key)
+ ), "PCA")
if (check == "No Result yet"){
output$PCA_Info <- renderText("PCA computed.")
pca_reactives$calculate <- 1
@@ -188,7 +188,7 @@ pca_Server <- function(id, data, params, row_select, updates){
if(pca_reactives$calculate >= 0){
# update the data if needed
# TODO check if the follwoing still needed as update is now done on 1st server level
- data2plot <- update_data(data, session_key)
+ data2plot <- update_data(session$token)
# select the neccesary data
if(input$data_selection_pca){
data2plot <- select_data(
@@ -320,9 +320,9 @@ pca_Server <- function(id, data, params, row_select, updates){
pca_reactives$df_loadings <- df_loadings
# assign res_temp
- res_tmp[[session_key]][["PCA"]] <<- list(pca)
+ res_tmp[[session$token]][["PCA"]] <<- list(pca)
# assign par_temp as empty list
- par_tmp[[session_key]][["PCA"]] <<- list(
+ par_tmp[[session$token]][["PCA"]] <<- list(
# add a dummy parameter to avoid error
dummy = "dummy",
sample_selection_pca = input$sample_selection_pca,
diff --git a/program/shinyApp/R/pca/util.R b/program/shinyApp/R/pca/util.R
index 23135161..8fa4719d 100644
--- a/program/shinyApp/R/pca/util.R
+++ b/program/shinyApp/R/pca/util.R
@@ -1,9 +1,9 @@
-check_calculations <- function(current_parameters, module, session_key){
- if (is.null(res_tmp[[session_key]][[module]])){ # chec whether result is existent
+check_calculations <- function(current_parameters, module){
+ if (is.null(res_tmp[[session$token]][[module]])){ # chec whether result is existent
return("No Result yet")
}
# check whether all parameters are identical to the current existing result
- if (identical(par_tmp[[session_key]][[module]], current_parameters)){
+ if (identical(par_tmp[[session$token]][[module]], current_parameters)){
return("Result exists")
}
# The remaining case is an existing result with other parameters,
diff --git a/program/shinyApp/R/sample_correlation/server.R b/program/shinyApp/R/sample_correlation/server.R
index 4212398f..b0d7e616 100644
--- a/program/shinyApp/R/sample_correlation/server.R
+++ b/program/shinyApp/R/sample_correlation/server.R
@@ -40,7 +40,7 @@ sample_correlation_server <- function(id, data, params, updates){
if(sample_corr_reactive$calculate == 1){
# update the data if needed
- data <- update_data(data, session_key)
+ data <- update_data(session$token)
sample_corr_reactive$current_updates <- updates()
# set the counter to 0 to prevent any further plotting
sample_corr_reactive$calculate <- 0
@@ -53,10 +53,10 @@ sample_correlation_server <- function(id, data, params, updates){
data_info = list(
rows = length(rownames(data$data)),
cols = length(colnames(data$data)),
- preprocessing = par_tmp[[session_key]]$PreProcessing_Procedure
+ preprocessing = par_tmp[[session$token]]$PreProcessing_Procedure
)
),
- "SampleCorrelation", session_key
+ "SampleCorrelation"
)
if (check == "No Result yet"){
output$SampleCorr_Info <- renderText(
@@ -70,7 +70,7 @@ sample_correlation_server <- function(id, data, params, updates){
output$SampleCorr_Info <- renderText(
"Correlation Matrix was already computed, no need to click the Button again."
)
- cormat <- res_tmp[[session_key]]$SampleCorrelation
+ cormat <- res_tmp[[session$token]]$SampleCorrelation
} else if (check == "Overwrite"){
output$SampleCorr_Info <- renderText(
"Correlation Matrix result overwritten with different parameters."
@@ -122,14 +122,14 @@ sample_correlation_server <- function(id, data, params, updates){
annotation_colors = anno_colors
)
# assign res_temp["SampleCorrelation"]
- res_tmp[[session_key]][["SampleCorrelation"]] <<- cormat
+ res_tmp[[session$token]][["SampleCorrelation"]] <<- cormat
# assign par_temp["SampleCorrelation"]
- par_tmp[[session_key]][["SampleCorrelation"]] <<- list(
+ par_tmp[[session$token]][["SampleCorrelation"]] <<- list(
corrMethod = input$corrMethod,
data_info = list(
rows = length(rownames(data$data)),
cols = length(colnames(data$data)),
- preprocessing = par_tmp[[session_key]]$PreProcessing_Procedure
+ preprocessing = par_tmp[[session$token]]$PreProcessing_Procedure
)
)
@@ -141,7 +141,7 @@ sample_correlation_server <- function(id, data, params, updates){
customTitleSampleCorrelation <- "SampleCorrelation"
}
- par_tmp[[session_key]][["SampleCorr"]] <<- list(
+ par_tmp[[session$token]][["SampleCorr"]] <<- list(
customTitleSampleCorrelation = customTitleSampleCorrelation,
SampleCorrelationPlot_final = SampleCorrelationPlot_final,
cormat = cormat,
@@ -161,16 +161,16 @@ sample_correlation_server <- function(id, data, params, updates){
},
content = function(file){
envList = list(
- cormat = ifelse(exists("cormat"),par_tmp[[session_key]][["SampleCorr"]]$cormat,NA),
- annotationDF = ifelse(exists("annotationDF"),par_tmp[[session_key]][["SampleCorr"]]$annotationDF,NA),
- customTitleSampleCorrelation = ifelse(exists("customTitleSampleCorrelation"),par_tmp[[session_key]][["SampleCorr"]]$customTitleSampleCorrelation,NA),
- anno_colors = ifelse(exists("anno_colors"),par_tmp[[session_key]][["SampleCorr"]]$anno_colors,NA)
+ cormat = ifelse(exists("cormat"),par_tmp[[session$token]][["SampleCorr"]]$cormat,NA),
+ annotationDF = ifelse(exists("annotationDF"),par_tmp[[session$token]][["SampleCorr"]]$annotationDF,NA),
+ customTitleSampleCorrelation = ifelse(exists("customTitleSampleCorrelation"),par_tmp[[session$token]][["SampleCorr"]]$customTitleSampleCorrelation,NA),
+ anno_colors = ifelse(exists("anno_colors"),par_tmp[[session$token]][["SampleCorr"]]$anno_colors,NA)
)
temp_directory <- file.path(tempdir(), as.integer(Sys.time()))
dir.create(temp_directory)
- write(getPlotCode(par_tmp[[session_key]][["SampleCorr"]]$sampleCorrelation_scenario), file.path(temp_directory, "Code.R"))
+ write(getPlotCode(par_tmp[[session$token]][["SampleCorr"]]$sampleCorrelation_scenario), file.path(temp_directory, "Code.R"))
saveRDS(envList, file.path(temp_directory, "Data.RDS"))
zip::zip(
@@ -184,18 +184,18 @@ sample_correlation_server <- function(id, data, params, updates){
output$SavePlot_SampleCorrelation <- downloadHandler(
filename = function() {
- paste(par_tmp[[session_key]][["SampleCorr"]]$customTitleSampleCorrelation,Sys.time(),input$file_ext_Heatmap,sep = "")
+ paste(par_tmp[[session$token]][["SampleCorr"]]$customTitleSampleCorrelation,Sys.time(),input$file_ext_Heatmap,sep = "")
},
content = function(file){
- save_pheatmap(par_tmp[[session_key]][["SampleCorr"]]$SampleCorrelationPlot_final,filename = file,type=gsub("\\.","",input$file_ext_SampleCorrelation))
+ save_pheatmap(par_tmp[[session$token]][["SampleCorr"]]$SampleCorrelationPlot_final,filename = file,type=gsub("\\.","",input$file_ext_SampleCorrelation))
on.exit({
tmp_filename <- paste0(
getwd(),
"/www/",
- paste(paste(par_tmp[[session_key]][["SampleCorr"]]$customTitleSampleCorrelation,Sys.time(),input$file_ext_SampleCorrelation,sep = ""))
+ paste(paste(par_tmp[[session$token]][["SampleCorr"]]$customTitleSampleCorrelation,Sys.time(),input$file_ext_SampleCorrelation,sep = ""))
)
save_pheatmap(
- par_tmp[[session_key]][["SampleCorr"]]$SampleCorrelationPlot_final,
+ par_tmp[[session$token]][["SampleCorr"]]$SampleCorrelationPlot_final,
filename = tmp_filename,
type = gsub("\\.","",input$file_ext_SampleCorrelation)
)
@@ -216,11 +216,11 @@ sample_correlation_server <- function(id, data, params, updates){
tmp_filename <- paste0(
getwd(),
"/www/",
- paste(paste(par_tmp[[session_key]][["SampleCorr"]]$customTitleSampleCorrelation,Sys.time(),".png",sep = ""))
+ paste(paste(par_tmp[[session$token]][["SampleCorr"]]$customTitleSampleCorrelation,Sys.time(),".png",sep = ""))
)
save_pheatmap(
- par_tmp[[session_key]][["SampleCorr"]]$SampleCorrelationPlot_final,
+ par_tmp[[session$token]][["SampleCorr"]]$SampleCorrelationPlot_final,
filename = tmp_filename,
type = "png"
)
diff --git a/program/shinyApp/R/significance_analysis/server.R b/program/shinyApp/R/significance_analysis/server.R
index 1622c0a9..c9364996 100644
--- a/program/shinyApp/R/significance_analysis/server.R
+++ b/program/shinyApp/R/significance_analysis/server.R
@@ -181,8 +181,8 @@ significance_analysis_server <- function(id, data, params, updates){
)
# refresh the UI/data if needed
observeEvent(input$refreshUI, {
- data <- update_data(data, session_key)
- params <- update_params(params, session_key)
+ data <- update_data(session$token)
+ params <- update_params(session$token)
sig_ana_reactive$current_updates <- updates()
sig_ana_reactive$coldata <- colData(data$data)
})
@@ -201,7 +201,7 @@ significance_analysis_server <- function(id, data, params, updates){
}
print("Start the Significance Analysis")
# update the data if needed
- data <- update_data(data, session_key)
+ data <- update_data(session$token)
sig_ana_reactive$current_updates <- updates()
sig_ana_reactive$coldata <- colData(data$data)
# delete old panels
@@ -229,10 +229,10 @@ significance_analysis_server <- function(id, data, params, updates){
for (i in 1:length(contrasts)) {
if(identical(
list(test_method = "Wald", test_correction = PADJUST_METHOD[[input$test_correction]]),
- par_tmp[[session_key]]$SigAna[[input$sample_annotation_types_cmp]][[input$comparisons[i]]]
+ par_tmp[[session$token]]$SigAna[[input$sample_annotation_types_cmp]][[input$comparisons[i]]]
)){
print("Results exists, skipping calculations.")
- sig_results[[input$comparisons[i]]] <<- res_tmp[[session_key]]$SigAna[[input$sample_annotation_types_cmp]][[input$comparisons[i]]]
+ sig_results[[input$comparisons[i]]] <<- res_tmp[[session$token]]$SigAna[[input$sample_annotation_types_cmp]][[input$comparisons[i]]]
next
}
sig_results[[input$comparisons[i]]] <<- DESeq2::results(
@@ -244,9 +244,9 @@ significance_analysis_server <- function(id, data, params, updates){
),
pAdjustMethod = PADJUST_METHOD[[input$test_correction]]
)
- # fill in res_tmp[[session_key]], par_tmp[[session_key]]
- res_tmp[[session_key]]$SigAna[[input$sample_annotation_types_cmp]][[input$comparisons[i]]] <<- sig_results[[input$comparisons[i]]]
- par_tmp[[session_key]]$SigAna[[input$sample_annotation_types_cmp]][[input$comparisons[i]]] <<- list(
+ # fill in res_tmp[[session$token]], par_tmp[[session$token]]
+ res_tmp[[session$token]]$SigAna[[input$sample_annotation_types_cmp]][[input$comparisons[i]]] <<- sig_results[[input$comparisons[i]]]
+ par_tmp[[session$token]]$SigAna[[input$sample_annotation_types_cmp]][[input$comparisons[i]]] <<- list(
test_method = "Wald",
test_correction = PADJUST_METHOD[[input$test_correction]]
)
diff --git a/program/shinyApp/R/significance_analysis/util.R b/program/shinyApp/R/significance_analysis/util.R
index 913b4427..9567073f 100644
--- a/program/shinyApp/R/significance_analysis/util.R
+++ b/program/shinyApp/R/significance_analysis/util.R
@@ -811,10 +811,10 @@ significance_analysis <- function(
# skip if already there
if(identical(
list(test_method = method, test_correction = correction),
- par_tmp[[session_key]]$SigAna[[contrast_level]][[names(contrasts)[comp_name]]]
+ par_tmp[[session$token]]$SigAna[[contrast_level]][[names(contrasts)[comp_name]]]
)){
print("Results exists, skipping calculations.")
- sig_results[[names(contrasts)[comp_name]]] <- res_tmp[[session_key]]$SigAna[[contrast_level]][[names(contrasts)[comp_name]]]
+ sig_results[[names(contrasts)[comp_name]]] <- res_tmp[[session$token]]$SigAna[[contrast_level]][[names(contrasts)[comp_name]]]
comp_name <- comp_name + 1
next
}
@@ -850,9 +850,9 @@ significance_analysis <- function(
sig_results[[names(contrasts)[comp_name]]] <- res
- # fill res_tmp[[session_key]], par_tmp[[session_key]]
- res_tmp[[session_key]]$SigAna[[contrast_level]][[names(contrasts)[comp_name]]] <<- res
- par_tmp[[session_key]]$SigAna[[contrast_level]][[names(contrasts)[comp_name]]] <<- list(
+ # fill res_tmp[[session$token]], par_tmp[[session$token]]
+ res_tmp[[session$token]]$SigAna[[contrast_level]][[names(contrasts)[comp_name]]] <<- res
+ par_tmp[[session$token]]$SigAna[[contrast_level]][[names(contrasts)[comp_name]]] <<- list(
test_method = method,
test_correction = correction
)
@@ -925,9 +925,9 @@ getLFC <- function(means){
)
return (df$LFC)
}
- if(par_tmp[[session_key]]$PreProcessing_Procedure == "log10"){
+ if(par_tmp[[session$token]]$PreProcessing_Procedure == "log10"){
lfc_per_gene_log(means, log_base = 10)
- }else if(par_tmp[[session_key]]$PreProcessing_Procedure == "ln"){
+ }else if(par_tmp[[session$token]]$PreProcessing_Procedure == "ln"){
lfc_per_gene_log(means, log_base = exp(1))
}else{
lfc_per_gene(means)
diff --git a/program/shinyApp/R/single_gene_visualisation/server.R b/program/shinyApp/R/single_gene_visualisation/server.R
index 64d43d5e..40d0b418 100644
--- a/program/shinyApp/R/single_gene_visualisation/server.R
+++ b/program/shinyApp/R/single_gene_visualisation/server.R
@@ -16,8 +16,8 @@ single_gene_visualisation_server <- function(id, data, params, updates){
# Refresh UI /Data
observeEvent(input$refreshUI,{
print("Refresh UI Single Gene")
- data <- update_data(data, session_key)
- params <- update_params(params, session_key)
+ data <- update_data(session$token)
+ params <- update_params(session$token)
single_Gene_vis$current_updates <- updates()
## Ui section ----
@@ -129,7 +129,7 @@ single_gene_visualisation_server <- function(id, data, params, updates){
print(input$Select_Gene)
if(single_Gene_vis$calculate == 1){
# update the data if needed
- data <- update_data(data, session_key)
+ data <- update_data(session$token)
single_Gene_vis$current_updates <- updates()
# set the counter to 0 to prevent any further plotting
single_Gene_vis$calculate <- 0
@@ -254,11 +254,11 @@ single_gene_visualisation_server <- function(id, data, params, updates){
}
# Where to save the plot (needed currently to be global, to be able to be saved)
- res_tmp[[session_key]][["SingleEntVis"]] <<- P_boxplots
+ res_tmp[[session$token]][["SingleEntVis"]] <<- P_boxplots
#SingleEnt_P_boxplots <- P_boxplots
- # DO not know if necassary to track in par_tmp[[session_key]] (if not global var needed)
- par_tmp[[session_key]][["SingleEntVis"]] <<- list(
+ # DO not know if necassary to track in par_tmp[[session$token]] (if not global var needed)
+ par_tmp[[session$token]][["SingleEntVis"]] <<- list(
SingleEnt_customTitle_boxplot = SingleEnt_customTitle_boxplot,
SingleEnt_Select_Gene = input$Select_Gene,
SingleEnt_type_of_data_gene = input$type_of_data_gene,
@@ -306,7 +306,7 @@ single_gene_visualisation_server <- function(id, data, params, updates){
output$SavePlot_singleGene <- downloadHandler(
filename = function() {
paste(
- par_tmp[[session_key]]$SingleEntVis$SingleEnt_customTitle_boxplot,
+ par_tmp[[session$token]]$SingleEntVis$SingleEnt_customTitle_boxplot,
" ",
Sys.time(),
input$file_ext_singleGene,sep=""
@@ -316,7 +316,7 @@ single_gene_visualisation_server <- function(id, data, params, updates){
content = function(file){
ggsave(
file = file,
- plot = res_tmp[[session_key]]$SingleEntVis,
+ plot = res_tmp[[session$token]]$SingleEntVis,
device = gsub("\\.","",input$file_ext_singleGene)
)
@@ -325,14 +325,14 @@ single_gene_visualisation_server <- function(id, data, params, updates){
getwd(),
"/www/",
paste(
- par_tmp[[session_key]]$SingleEntVis$SingleEnt_customTitle_boxplot,
+ par_tmp[[session$token]]$SingleEntVis$SingleEnt_customTitle_boxplot,
" ",
Sys.time(),
input$file_ext_singleGene,sep="")
)
ggsave(
filename = tmp_filename,
- plot = res_tmp[[session_key]]$SingleEntVis,
+ plot = res_tmp[[session$token]]$SingleEntVis,
device = gsub("\\.","",input$file_ext_singleGene)
)
fun_LogIt("## Single Entitie")
@@ -360,7 +360,7 @@ single_gene_visualisation_server <- function(id, data, params, updates){
getwd(),
"/www/",
paste(
- par_tmp[[session_key]]$SingleEntVis$SingleEnt_customTitle_boxplot,
+ par_tmp[[session$token]]$SingleEntVis$SingleEnt_customTitle_boxplot,
" ",
Sys.time(),
".png",
@@ -368,27 +368,27 @@ single_gene_visualisation_server <- function(id, data, params, updates){
)
ggsave(
filename = tmp_filename,
- plot = res_tmp[[session_key]]$SingleEntVis,
+ plot = res_tmp[[session$token]]$SingleEntVis,
device = "png"
)
fun_LogIt(message = "## Single Entitie")
fun_LogIt(message = paste0(
"**Single Entitie** - The following single entitie was plotted: ",
- par_tmp[[session_key]]$SingleEntVis$SingleEnt_Select_Gene))
+ par_tmp[[session$token]]$SingleEntVis$SingleEnt_Select_Gene))
fun_LogIt(message = paste0(
"**Single Entitie** - Values shown are: ",
- par_tmp[[session_key]]$SingleEntVis$SingleEnt_type_of_data_gene, " data input"))
+ par_tmp[[session$token]]$SingleEntVis$SingleEnt_type_of_data_gene, " data input"))
fun_LogIt(message = paste0(
"**Single Entitie** - Values are grouped for all levels within: ",
- par_tmp[[session_key]]$SingleEntVis$SingleEnt_accross_condition,
+ par_tmp[[session$token]]$SingleEntVis$SingleEnt_accross_condition,
" (",
- paste0(levels(par_tmp[[session_key]]$SingleEntVis$SingleEnt_GeneData_anno),collapse = ";")
+ paste0(levels(par_tmp[[session$token]]$SingleEntVis$SingleEnt_GeneData_anno),collapse = ";")
,")"))
fun_LogIt(message = paste0(
"**Single Entitie** - Test for differences: ",
- par_tmp[[session_key]]$SingleEntVis$SingleEnt_testMethod))
+ par_tmp[[session$token]]$SingleEntVis$SingleEnt_testMethod))
- if(length(levels(par_tmp[[session_key]]$SingleEntVis$SingleEnt_GeneData_anno))>2){
+ if(length(levels(par_tmp[[session$token]]$SingleEntVis$SingleEnt_GeneData_anno))>2){
fun_LogIt(
message = paste0("**Single Entitie** - ANOVA performed, reference group is the overall mean")
)
diff --git a/program/shinyApp/R/util.R b/program/shinyApp/R/util.R
index 58d390dd..62df1bcf 100644
--- a/program/shinyApp/R/util.R
+++ b/program/shinyApp/R/util.R
@@ -1,10 +1,10 @@
### general utility functions will be defined here
-update_data <- function(data, session_key){
+update_data <- function(session_id){
# for stability reasons, data is ALWAYS pulled here
print("Updating data...")
- data <- res_tmp[[session_key]]
+ data <- res_tmp[[session_id]]
return(data)
}
@@ -27,11 +27,11 @@ select_data <- function(data, selected_samples, sample_type){
}
-update_params <- function(params, session_key){
+update_params <- function(session_id){
# update parameter if updates is larger than current_updates
# could force to always update
print("Updating parameters...")
- params <- par_tmp[[session_key]]
+ params <- par_tmp[[session_id]]
return(params)
}
diff --git a/program/shinyApp/server.R b/program/shinyApp/server.R
index 5e5652d8..ef5ae465 100644
--- a/program/shinyApp/server.R
+++ b/program/shinyApp/server.R
@@ -4,9 +4,11 @@ server <- function(input,output,session){
global_Vars <<- reactiveValues() # OUTDATED?
- # session sepcific key
- session_key <- session$token
-
+ # fill session_if textOutput with current session$token
+ output$session_id <- renderText({
+ paste0("Current session: ", session$token)
+ })
+
# getCurrentVersion(updateDESCRIPTION=T) # Where to Place this ? So it does not always get 'updated'?
# Can we add this somehow as necassary to every new release?
@@ -75,9 +77,15 @@ server <- function(input,output,session){
res_tmp <<- list()
par_tmp <<- list()
}
- # create an empty list in res/par_tmp[[session_key]]
- res_tmp[[session_key]] <<- list()
- par_tmp[[session_key]] <<- list()
+ # create an empty list in res/par_tmp[[session$token]]
+ res_tmp[[session$token]] <<- list()
+ par_tmp[[session$token]] <<- list()
+ # On session end, remove the list from res/par_tmp
+ session$onSessionEnded(function() {
+ res_tmp[[session$token]] <<- NULL
+ par_tmp[[session$token]] <<- NULL
+ })
+ browser()
# Init update Object ----
# updating is a reative value that counts up whenever data is updated
# this is used to trigger the update of the servers
@@ -194,7 +202,7 @@ server <- function(input,output,session){
content = function(file){
# TODO Q: What to save here? only original enough?
saveRDS(
- object = res_tmp[[session_key]]$data_original,
+ object = res_tmp[[session$token]]$data_original,
file = file
)
}
@@ -352,11 +360,11 @@ server <- function(input,output,session){
## Do Upload ----
observeEvent(input$refresh1,{
- par_tmp[[session_key]]['omic_type'] <<- input$omicType
+ par_tmp[[session$token]]['omic_type'] <<- input$omicType
fun_LogIt(message = "## DataInput {.tabset .tabset-fade}")
fun_LogIt(message = "### Info")
fun_LogIt(
- message = paste0("**DataInput** - Uploaded Omic Type: ", par_tmp[[session_key]]['omic_type'])
+ message = paste0("**DataInput** - Uploaded Omic Type: ", par_tmp[[session$token]]['omic_type'])
)
if(!(isTruthy(input$data_preDone) |
FLAG_TEST_DATA_SELECTED() |
@@ -368,8 +376,8 @@ server <- function(input,output,session){
output$debug <- renderText({"The Test Data Set was used"})
}else{
show_toast(
- title = paste0(par_tmp[[session_key]]['omic_type'],"Data Upload"),
- text = paste0(par_tmp[[session_key]]['omic_type'],"-data upload was successful"),
+ title = paste0(par_tmp[[session$token]]['omic_type'],"Data Upload"),
+ text = paste0(par_tmp[[session$token]]['omic_type'],"-data upload was successful"),
position = "top",
timer = 1500,
timerProgressBar = T
@@ -498,32 +506,32 @@ server <- function(input,output,session){
#TODO make the copy and tab show process dependent if we get here a results object or 'simple' rds
}
# TODO SumExp only needed hence more restructuring needed
- res_tmp[[session_key]][['data_original']] <<- data_input[[paste0(input$omicType,"_SumExp")]]
+ res_tmp[[session$token]][['data_original']] <<- data_input[[paste0(input$omicType,"_SumExp")]]
# Make a copy, to leave original data untouched
- res_tmp[[session_key]][['data']] <<- res_tmp[[session_key]]$data_original
+ res_tmp[[session$token]][['data']] <<- res_tmp[[session$token]]$data_original
# Count up updating
updating$count <- updating$count + 1
print(paste0(
- "(before) No. anno options sample_table: ",ncol(res_tmp[[session_key]]$data_original)
+ "(before) No. anno options sample_table: ",ncol(res_tmp[[session$token]]$data_original)
))
- colData(res_tmp[[session_key]]$data) <-
- DataFrame(as.data.frame(colData(res_tmp[[session_key]]$data)) %>%
+ colData(res_tmp[[session$token]]$data) <-
+ DataFrame(as.data.frame(colData(res_tmp[[session$token]]$data)) %>%
purrr::keep(~length(unique(.x)) != 1))
print(paste0(
- "(after) No. anno options sample_table: ",ncol(res_tmp[[session_key]]$data)
+ "(after) No. anno options sample_table: ",ncol(res_tmp[[session$token]]$data)
))
print(paste0(
- "(before) No. anno options annotation_rows: ",ncol(res_tmp[[session_key]]$data_original)
+ "(before) No. anno options annotation_rows: ",ncol(res_tmp[[session$token]]$data_original)
))
- rowData(res_tmp[[session_key]]$data) <-
- DataFrame(as.data.frame(rowData(res_tmp[[session_key]]$data)) %>%
+ rowData(res_tmp[[session$token]]$data) <-
+ DataFrame(as.data.frame(rowData(res_tmp[[session$token]]$data)) %>%
purrr::keep(~length(unique(.x)) != 1))
print(paste0(
- "(after) No. anno options annotation_rows: ",ncol(res_tmp[[session_key]]$data)
+ "(after) No. anno options annotation_rows: ",ncol(res_tmp[[session$token]]$data)
))
fun_LogIt(
@@ -532,13 +540,13 @@ server <- function(input,output,session){
)
fun_LogIt(
message = paste0("**DataInput** - The raw data dimensions are:",
- paste0(dim(res_tmp[[session_key]]$data_original),collapse = ", "))
+ paste0(dim(res_tmp[[session$token]]$data_original),collapse = ", "))
)
fun_LogIt(message = "### Publication Snippet")
fun_LogIt(message = snippet_dataInput(
- data_type = par_tmp[[session_key]]$omic_type,
- data_dimension = paste0(dim(res_tmp[[session_key]]$data_original),collapse = ", ")
+ data_type = par_tmp[[session$token]]$omic_type,
+ data_dimension = paste0(dim(res_tmp[[session$token]]$data_original),collapse = ", ")
))
fun_LogIt(message = "
")
return("DataUploadSuccesful")
@@ -550,14 +558,14 @@ server <- function(input,output,session){
## Ui Section ----
observe({
req(data_input_shiny())
- isTruthy(res_tmp[[session_key]]$data)
+ isTruthy(res_tmp[[session$token]]$data)
# Row
output$providedRowAnnotationTypes_ui=renderUI({
req(data_input_shiny())
shinyWidgets::virtualSelectInput(
inputId = "providedRowAnnotationTypes",
label = "Which annotation type do you want to select on?",
- choices = c(colnames(rowData(res_tmp[[session_key]]$data_original))),
+ choices = c(colnames(rowData(res_tmp[[session$token]]$data_original))),
multiple = F,
search = T,
showSelectedOptionsFirst = T
@@ -568,7 +576,7 @@ server <- function(input,output,session){
req(data_input_shiny())
req(input$providedRowAnnotationTypes)
if(is.numeric(
- rowData(res_tmp[[session_key]]$data_original)[,input$providedRowAnnotationTypes])
+ rowData(res_tmp[[session$token]]$data_original)[,input$providedRowAnnotationTypes])
){
selectInput(
inputId = "row_selection",
@@ -581,7 +589,7 @@ server <- function(input,output,session){
shinyWidgets::virtualSelectInput(
inputId = "row_selection",
label = "Which entities to use? (Will be the union if multiple selected)",
- choices = c("High Values+IQR","all",unique(unlist(strsplit(rowData(res_tmp[[session_key]]$data_original)[,input$providedRowAnnotationTypes],"\\|")))),
+ choices = c("High Values+IQR","all",unique(unlist(strsplit(rowData(res_tmp[[session$token]]$data_original)[,input$providedRowAnnotationTypes],"\\|")))),
selected = "all",
multiple = T,
search = T,
@@ -612,8 +620,8 @@ server <- function(input,output,session){
selectInput(
inputId = "providedSampleAnnotationTypes",
label = "Which annotation type do you want to select on?",
- choices = c(colnames(colData(res_tmp[[session_key]]$data_original))),
- selected = c(colnames(colData(res_tmp[[session_key]]$data_original)))[1],
+ choices = c(colnames(colData(res_tmp[[session$token]]$data_original))),
+ selected = c(colnames(colData(res_tmp[[session$token]]$data_original)))[1],
multiple = F
)
})
@@ -624,7 +632,7 @@ server <- function(input,output,session){
label = "Which entities to use? (Will be the union if multiple selected)",
choices = c(
"all",
- unique(colData(res_tmp[[session_key]]$data_original)[,input$providedSampleAnnotationTypes])
+ unique(colData(res_tmp[[session$token]]$data_original)[,input$providedSampleAnnotationTypes])
),
selected = "all",
multiple = T
@@ -677,17 +685,17 @@ server <- function(input,output,session){
## Do Selection ----
selectedData <- reactive({
shiny::req(input$row_selection, input$sample_selection)
- par_tmp[[session_key]][["row_selection"]] <<- input$row_selection
+ par_tmp[[session$token]][["row_selection"]] <<- input$row_selection
print("Alright do Row selection")
selected <- c()
if(any(input$row_selection == "all")){
- selected <- rownames(rowData(res_tmp[[session_key]]$data_original))
+ selected <- rownames(rowData(res_tmp[[session$token]]$data_original))
}else if(!(length(input$row_selection) == 1 & any(input$row_selection == "High Values+IQR"))){
selected <- unique(
c(selected,
- rownames(rowData(res_tmp[[session_key]]$data_original))[
- which(rowData(res_tmp[[session_key]]$data_original)[,input$providedRowAnnotationTypes]%in%input$row_selection)
+ rownames(rowData(res_tmp[[session$token]]$data_original))[
+ which(rowData(res_tmp[[session$token]]$data_original)[,input$providedRowAnnotationTypes]%in%input$row_selection)
]
)
)
@@ -695,17 +703,17 @@ server <- function(input,output,session){
if(any(input$row_selection == "High Values+IQR")){
if(length(input$row_selection) == 1){
toKeep <- filter_rna(
- rna = assay(res_tmp[[session_key]]$data_original),
+ rna = assay(res_tmp[[session$token]]$data_original),
prop = input$propensityChoiceUser
)
- filteredIQR_Expr <- assay(res_tmp[[session_key]]$data_original)[toKeep,]
+ filteredIQR_Expr <- assay(res_tmp[[session$token]]$data_original)[toKeep,]
selected <- rownames(filteredIQR_Expr)
}else{
toKeep <- filter_rna(
- rna = assay(res_tmp[[session_key]]$data_original)[selected,],
+ rna = assay(res_tmp[[session$token]]$data_original)[selected,],
prop = input$propensityChoiceUser
)
- filteredIQR_Expr <- assay(res_tmp[[session_key]]$data_original)[toKeep,]
+ filteredIQR_Expr <- assay(res_tmp[[session$token]]$data_original)[toKeep,]
selected <- intersect(
selected,
rownames(filteredIQR_Expr)
@@ -717,20 +725,20 @@ server <- function(input,output,session){
# Column Selection
samples_selected <- c()
if(any(input$sample_selection == "all")){
- samples_selected <- colnames(assay(res_tmp[[session_key]]$data_original))
+ samples_selected <- colnames(assay(res_tmp[[session$token]]$data_original))
}else{
samples_selected <- c(
samples_selected,
- rownames(colData(res_tmp[[session_key]]$data_original))[which(
- colData(res_tmp[[session_key]]$data_original)[,input$providedSampleAnnotationTypes] %in% input$sample_selection
+ rownames(colData(res_tmp[[session$token]]$data_original))[which(
+ colData(res_tmp[[session$token]]$data_original)[,input$providedSampleAnnotationTypes] %in% input$sample_selection
)]
)
}
# Data set selection
print("Alright do Column selection")
- res_tmp[[session_key]]$data <<- res_tmp[[session_key]]$data_original[selected,samples_selected]
- tmp_data_selected <<- res_tmp[[session_key]]$data_original[selected,samples_selected]
+ res_tmp[[session$token]]$data <<- res_tmp[[session$token]]$data_original[selected,samples_selected]
+ tmp_data_selected <<- res_tmp[[session$token]]$data_original[selected,samples_selected]
return("Selection Success")
})
@@ -811,42 +819,42 @@ server <- function(input,output,session){
print("Do Preprocessing")
print(selectedData())
addWarning <- ""
- par_tmp[[session_key]]['PreProcessing_Procedure'] <<- input$PreProcessing_Procedure
+ par_tmp[[session$token]]['PreProcessing_Procedure'] <<- input$PreProcessing_Procedure
processedData_all <- tmp_data_selected
# as general remove all genes which are constant over all rows
print("As general remove all entities which are constant over all samples")
- res_tmp[[session_key]]$data <<- tmp_data_selected[rownames(tmp_data_selected[which(apply(assay(tmp_data_selected),1,sd) != 0),]),]
+ res_tmp[[session$token]]$data <<- tmp_data_selected[rownames(tmp_data_selected[which(apply(assay(tmp_data_selected),1,sd) != 0),]),]
- print(dim(res_tmp[[session_key]]$data))
+ print(dim(res_tmp[[session$token]]$data))
# explicitly set rownames to avoid any errors.
- # new object Created for res_tmp[[session_key]]
- res_tmp[[session_key]]$data <<- res_tmp[[session_key]]$data[rownames(res_tmp[[session_key]]$data),]
+ # new object Created for res_tmp[[session$token]]
+ res_tmp[[session$token]]$data <<- res_tmp[[session$token]]$data[rownames(res_tmp[[session$token]]$data),]
if(input$PreProcessing_Procedure != "none"){
if(input$PreProcessing_Procedure == "filterOnly"){
- if(par_tmp[[session_key]]$omic_type == "Transcriptomics"){
+ if(par_tmp[[session$token]]$omic_type == "Transcriptomics"){
print("Also remove anything of rowCount <=10")
print(dim(tmp_data_selected))
- res_tmp[[session_key]]$data <<- tmp_data_selected[which(rowSums(assay(tmp_data_selected)) > 10),]
+ res_tmp[[session$token]]$data <<- tmp_data_selected[which(rowSums(assay(tmp_data_selected)) > 10),]
}
- if(par_tmp[[session_key]]$omic_type == "Metabolomics"){
+ if(par_tmp[[session$token]]$omic_type == "Metabolomics"){
print("Remove anything which has a row median of 0")
print(dim(tmp_data_selected))
- res_tmp[[session_key]]$data <<- tmp_data_selected[which(apply(assay(tmp_data_selected),1,median)!=0),]
+ res_tmp[[session$token]]$data <<- tmp_data_selected[which(apply(assay(tmp_data_selected),1,median)!=0),]
}
addWarning <- "Only Filtering of low abundant is done only if Transcriptomics or Metabolomics was chosen\n"
}else{
- if(par_tmp[[session_key]]$omic_type == "Transcriptomics"){
+ if(par_tmp[[session$token]]$omic_type == "Transcriptomics"){
print("Also remove anything of rowCount <=10")
print(dim(tmp_data_selected))
- res_tmp[[session_key]]$data <<- tmp_data_selected[which(rowSums(assay(tmp_data_selected)) > 10),]
+ res_tmp[[session$token]]$data <<- tmp_data_selected[which(rowSums(assay(tmp_data_selected)) > 10),]
}
- if(par_tmp[[session_key]]$omic_type == "Metabolomics"){
+ if(par_tmp[[session$token]]$omic_type == "Metabolomics"){
print("Remove anything which has a row median of 0")
print(dim(tmp_data_selected))
@@ -854,27 +862,27 @@ server <- function(input,output,session){
}
}
- print(dim(res_tmp[[session_key]]$data))
+ print(dim(res_tmp[[session$token]]$data))
print(paste0("Do chosen Preprocessing:",input$PreProcessing_Procedure))
if(input$PreProcessing_Procedure == "simpleCenterScaling"){
processedData <- as.data.frame(t(
scale(
- x = as.data.frame(t(as.data.frame(assay(res_tmp[[session_key]]$data)))),
+ x = as.data.frame(t(as.data.frame(assay(res_tmp[[session$token]]$data)))),
scale = T,
center = T
)
)
)
- assay(res_tmp[[session_key]]$data) <<- as.data.frame(processedData)
+ assay(res_tmp[[session$token]]$data) <<- as.data.frame(processedData)
}
if(input$PreProcessing_Procedure == "vst_DESeq"){
- par_tmp[[session_key]]["DESeq_advanced"] <<- FALSE
- if(par_tmp[[session_key]]$omic_type == "Transcriptomics"){
+ par_tmp[[session$token]]["DESeq_advanced"] <<- FALSE
+ if(par_tmp[[session$token]]$omic_type == "Transcriptomics"){
design_formula <- paste("~", input$DESeq_formula_main)
# only do this locally
- colData(res_tmp[[session_key]]$data)[,input$DESeq_formula_main] <- as.factor(
- colData(res_tmp[[session_key]]$data)[,input$DESeq_formula_main]
+ colData(res_tmp[[session$token]]$data)[,input$DESeq_formula_main] <- as.factor(
+ colData(res_tmp[[session$token]]$data)[,input$DESeq_formula_main]
)
if(length(input$DESeq_formula_sub) > 0){
design_formula <- paste(
@@ -883,63 +891,63 @@ server <- function(input,output,session){
)
# turn each factor into a factor
for(i in input$DESeq_formula_sub){
- colData(res_tmp[[session_key]]$data)[,i] <- as.factor(
- colData(res_tmp[[session_key]]$data)[,i]
+ colData(res_tmp[[session$token]]$data)[,i] <- as.factor(
+ colData(res_tmp[[session$token]]$data)[,i]
)
}
- par_tmp[[session_key]][["DESeq_factors"]] <<- c(
+ par_tmp[[session$token]][["DESeq_factors"]] <<- c(
input$DESeq_formula_main,input$DESeq_formula_sub
)
}
else{
- par_tmp[[session_key]][["DESeq_factors"]] <<- c(input$DESeq_formula_main)
+ par_tmp[[session$token]][["DESeq_factors"]] <<- c(input$DESeq_formula_main)
}
# if advanced formula is used, overwrite the other formula
if(input$DESeq_show_advanced){
if(startsWith(input$DESeq_formula_advanced, "~")){
print("Advanced formula used")
design_formula <- input$DESeq_formula_advanced
- par_tmp[[session_key]]["DESeq_advanced"] <<- TRUE
+ par_tmp[[session$token]]["DESeq_advanced"] <<- TRUE
}
}
print(design_formula)
- par_tmp[[session_key]]["DESeq_formula"] <<- design_formula
+ par_tmp[[session$token]]["DESeq_formula"] <<- design_formula
# on purpose local
- print(colData(res_tmp[[session_key]]$data)[,input$DESeq_formula_main])
+ print(colData(res_tmp[[session$token]]$data)[,input$DESeq_formula_main])
dds <- DESeq2::DESeqDataSetFromMatrix(
- countData = assay(res_tmp[[session_key]]$data),
- colData = colData(res_tmp[[session_key]]$data),
+ countData = assay(res_tmp[[session$token]]$data),
+ colData = colData(res_tmp[[session$token]]$data),
design = as.formula(design_formula)
)
de_seq_result <- DESeq2::DESeq(dds)
- res_tmp[[session_key]]$DESeq_obj <<- de_seq_result
+ res_tmp[[session$token]]$DESeq_obj <<- de_seq_result
dds_vst <- vst(
object = de_seq_result,
blind = TRUE
)
- assay(res_tmp[[session_key]]$data) <<- as.data.frame(assay(dds_vst))
+ assay(res_tmp[[session$token]]$data) <<- as.data.frame(assay(dds_vst))
}else{
addWarning <- "DESeq makes only sense for transcriptomics data - data treated as if 'none' was selected!"
}
}
if(input$PreProcessing_Procedure == "Scaling_0_1"){
processedData <- as.data.frame(t(
- apply(assay(res_tmp[[session_key]]$data),1,function(x){
+ apply(assay(res_tmp[[session$token]]$data),1,function(x){
(x - min(x))/(max(x) - min(x))
})
))
- assay(res_tmp[[session_key]]$data) <<- as.data.frame(processedData)
+ assay(res_tmp[[session$token]]$data) <<- as.data.frame(processedData)
}
if(input$PreProcessing_Procedure == "ln"){
processedData <- as.data.frame(log(
- as.data.frame(assay(res_tmp[[session_key]]$data))
+ as.data.frame(assay(res_tmp[[session$token]]$data))
))
- assay(res_tmp[[session_key]]$data) <<- as.data.frame(processedData)
+ assay(res_tmp[[session$token]]$data) <<- as.data.frame(processedData)
}
if(input$PreProcessing_Procedure == "log10"){
- processedData <- as.data.frame(assay(res_tmp[[session_key]]$data))
+ processedData <- as.data.frame(assay(res_tmp[[session$token]]$data))
if(any(processedData<0)){
addWarning <- "Negative entries, cannot take log10!!"
}
@@ -951,10 +959,10 @@ server <- function(input,output,session){
processedData <- as.data.frame(log10(
processedData + 1)
)
- assay(res_tmp[[session_key]]$data) <<- as.data.frame(processedData)
+ assay(res_tmp[[session$token]]$data) <<- as.data.frame(processedData)
}
if(input$PreProcessing_Procedure == "pareto_scaling"){
- processedData <- as.data.frame(assay(res_tmp[[session_key]]$data))
+ processedData <- as.data.frame(assay(res_tmp[[session$token]]$data))
centered <- as.data.frame(t(
apply(processedData, 1, function(x){x - mean(x)})
))
@@ -962,24 +970,24 @@ server <- function(input,output,session){
apply(centered, 1, function(x){x/sqrt(sd(x))})
))
- assay(res_tmp[[session_key]]$data) <<- as.data.frame(pareto.matrix)
+ assay(res_tmp[[session$token]]$data) <<- as.data.frame(pareto.matrix)
}
}
- if(any(is.na(assay(res_tmp[[session_key]]$data)))){
+ if(any(is.na(assay(res_tmp[[session$token]]$data)))){
print("This might be problem due to mismatched Annotation Data?!")
- nrow_before <- nrow(assay(res_tmp[[session_key]]$data))
+ nrow_before <- nrow(assay(res_tmp[[session$token]]$data))
nrow_after <- nrow(
- res_tmp[[session_key]]$data[complete.cases(assay(res_tmp[[session_key]]$data)),]
+ res_tmp[[session$token]]$data[complete.cases(assay(res_tmp[[session$token]]$data)),]
)
addWarning <- paste0("There were NA's after pre-processing, any row containg such was completly removed! (before/after): ",nrow_before,"/",nrow_after,"")
if(!(nrow_after > 0)){
addWarning <- paste0(addWarning, "
There is nothing left, choose different pre-processing other-wise App will crash!")
}
- res_tmp[[session_key]]$data <<- res_tmp[[session_key]]$data[complete.cases(assay(res_tmp[[session_key]]$data)),]
+ res_tmp[[session$token]]$data <<- res_tmp[[session$token]]$data[complete.cases(assay(res_tmp[[session$token]]$data)),]
}
- print(colnames(res_tmp[[session_key]]$data))
+ print(colnames(res_tmp[[session$token]]$data))
showTab(inputId = "tabsetPanel1", target = "Sample Correlation")
showTab(inputId = "tabsetPanel1", target = "Significance Analysis")
@@ -997,11 +1005,11 @@ server <- function(input,output,session){
shinyjs::click("single_gene_visualisation-refreshUI",asis = T)
paste0(addWarning,
"The data has the dimensions of: ",
- paste0(dim(res_tmp[[session_key]]$data),collapse = ", "),
+ paste0(dim(res_tmp[[session$token]]$data),collapse = ", "),
"
","Be aware that depending on omic-Type, basic pre-processing has been done anyway even when selecting none",
"",ifelse(any(as.data.frame(assay(res_tmp[[session_key]]$data)) < 0),"Be aware that processed data has negative values, hence no log fold changes can be calculated",""))
+ "
",ifelse(any(as.data.frame(assay(res_tmp[[session$token]]$data)) < 0),"Be aware that processed data has negative values, hence no log fold changes can be calculated",""))
})
@@ -1026,9 +1034,9 @@ server <- function(input,output,session){
## Log preprocessing ----
observeEvent(input$Do_preprocessing,{
print(selectedData_processed())
- if(par_tmp[[session_key]]$omic_type == "Transcriptomics"){
+ if(par_tmp[[session$token]]$omic_type == "Transcriptomics"){
tmp_logMessage <- "Remove anything which row Count <= 10"
- }else if(par_tmp[[session_key]]$omic_type == "Metabolomics"){
+ }else if(par_tmp[[session$token]]$omic_type == "Metabolomics"){
tmp_logMessage <- "Remove anything which has a row median of 0"
}else{
tmp_logMessage <- "none"
@@ -1046,20 +1054,20 @@ server <- function(input,output,session){
fun_LogIt(
message = paste0(
"**PreProcessing** - The resulting dimensions are: ",
- paste0(dim(res_tmp[[session_key]]$data),collapse = ", ")
+ paste0(dim(res_tmp[[session$token]]$data),collapse = ", ")
)
)
})
- output$debug <- renderText(dim(res_tmp[[session_key]]$data))
+ output$debug <- renderText(dim(res_tmp[[session$token]]$data))
## UP TILL HERE ##
# Sample Correlation ----
# calling server without reactive it will be init upon start, with no update
# of respective data inputs hence need of at least one reactive!
sample_correlation_server(
id = "sample_correlation",
- data = res_tmp[[session_key]],
- params = par_tmp[[session_key]],
+ data = res_tmp[[session$token]],
+ params = par_tmp[[session$token]],
reactive(updating$count)
#omic_type = reactive(input$omicType), # par_tmp$omic_type
#row_select = reactive(input$row_selection) #par_tmp$row_selection ? # only for title?
@@ -1068,30 +1076,30 @@ server <- function(input,output,session){
# significance analysis ----
significance_analysis_server(
id = 'SignificanceAnalysis',
- data = res_tmp[[session_key]],
- params = par_tmp[[session_key]],
+ data = res_tmp[[session$token]],
+ params = par_tmp[[session$token]],
reactive(updating$count)
)
# PCA ----
pca_Server(
id = "PCA",
- data = res_tmp[[session_key]],
- params = par_tmp[[session_key]],
+ data = res_tmp[[session$token]],
+ params = par_tmp[[session$token]],
reactive(input$row_selection),
reactive(updating$count)
)
# Heatmap ----
heatmap_server(
id = 'Heatmap',
- data = res_tmp[[session_key]],
- params = par_tmp[[session_key]],
+ data = res_tmp[[session$token]],
+ params = par_tmp[[session$token]],
reactive(updating$count)
)
# Single Gene Visualisations ----
single_gene_visualisation_server(
id = 'single_gene_visualisation',
- data = res_tmp[[session_key]],
- params = par_tmp[[session_key]],
+ data = res_tmp[[session$token]],
+ params = par_tmp[[session$token]],
reactive(updating$count)
)
@@ -1099,8 +1107,8 @@ server <- function(input,output,session){
# Enrichment Analysis ----
enrichment_analysis_Server(
id = 'EnrichmentAnalysis',
- data = res_tmp[[session_key]],
- params = par_tmp[[session_key]],
+ data = res_tmp[[session$token]],
+ params = par_tmp[[session$token]],
reactive(updating$count)
)
}
diff --git a/program/shinyApp/ui.R b/program/shinyApp/ui.R
index 2405b4e2..9697173f 100644
--- a/program/shinyApp/ui.R
+++ b/program/shinyApp/ui.R
@@ -185,6 +185,7 @@ ui <- shiny::fluidPage(
helpText("Metabolon Help", align = "center") %>% helper(type = "markdown", content = "Metabolon_help", size = "l", colour = "blue", style = "position: relative;top: -18px;left: 15px;; zoom: 200%;"),
NULL
),
+
tabsetPanel(
id = "tabsetPanel1",
################################################################################
@@ -241,6 +242,12 @@ ui <- shiny::fluidPage(
bottom = 0, left = 10, fixed = TRUE,style = "background-color: #a9d96a;"
)
)
+ ),
+ # Pannel displaying the current session id
+ absolutePanel(
+ # text output needs to be defined in server
+ textOutput("session_id"),
+ bottom = 0, right = 10, fixed = TRUE
)
)