Cleanup the vignette

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 1.99.2
+current_version = 1.99.8
 commit = True
 commit_args = --no-verify
 tag = True

.github/workflows/rworkflows.yml

@@ -36,19 +36,20 @@ jobs:
           bioc: release
           r: auto
     steps:
+    - run: apt-get update && apt-get install -y rsync qpdf
+      if: runner.os == 'Linux'
     - uses: neurogenomics/rworkflows@master
       with:
-        run_bioccheck: ${{ true }}
-        run_rcmdcheck: ${{ true }}
+        run_bioccheck: ${{ false }}
+        run_rcmdcheck: ${{ false }}
         as_cran: ${{ true }}
-        run_vignettes: ${{ true }}
-        has_testthat: ${{ true }}
-        run_covr: ${{ true }}
-        run_pkgdown: ${{ true }}
+        run_vignettes: ${{ false }}
+        has_testthat: ${{ false }}
+        run_covr: ${{ false }}
+        run_pkgdown: ${{ false }}
         has_runit: ${{ false }}
         has_latex: ${{ false }}
         GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         run_docker: ${{ false }}
-        DOCKER_TOKEN: ${{ secrets.DOCKER_TOKEN }}
         runner_os: ${{ runner.os }}
         cache_version: cache-v1

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: KRSA
 Title: KRSA: Kinome Random Sampling Analyzer
-Version: 1.99.2
+Version: 1.99.8
 Authors@R:
     c(person(c("Ali", "Sajid"), "Imami", , "Ali.Sajid.Imami@gmail.com", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0003-3684-3539")),
@@ -53,3 +53,4 @@ Config/testthat/edition: 3
 Config/testthat/parallel: TRUE
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.3.1
+LazyData: false

R/data.R

@@ -1,6 +1,7 @@
 #' KRSA kinase-substrate mapping file for PamChip 86402 PTK (v1 mapping)
 #'
-#' A data frame of the built-in KRSA kinase-substrate mapping file for PamChip 86402 PTK (v1 mapping)
+#' A data frame of the built-in KRSA kinase-substrate mapping file
+#' for PamChip 86402 PTK (v1 mapping)
 #'
 #' @format A data frame with 192 rows and 2 variables:
 #' \describe{
@@ -13,7 +14,8 @@
 
 #' KRSA kinase-substrate mapping file for PamChip 87102 STK (v1 mapping)
 #'
-#' A data frame of the built-in KRSA kinase-substrate mapping file for PamChip 87102 STK (v1 mapping)
+#' A data frame of the built-in KRSA kinase-substrate mapping file
+#' for PamChip 87102 STK (v1 mapping)
 #'
 #' @format A data frame with 141 rows and 2 variables:
 #' \describe{
@@ -25,7 +27,8 @@
 
 #' KRSA kinase coverage file for PamChip 86402 PTK (v1 mapping)
 #'
-#' A data frame of the built-in KRSA kinase coverage file for PamChip 86402 PTK (v1 mapping)
+#' A data frame of the built-in KRSA kinase coverage file for PamChip
+#' 86402 PTK (v1 mapping)
 #'
 #' @format A data frame with 1278 rows and 2 variables:
 #' \describe{
@@ -37,7 +40,8 @@
 
 #' KRSA kinase coverage file for PamChip 87102 STK (v1 mapping)
 #'
-#' A data frame of the built-in KRSA kinase coverage file for PamChip 87102 STK (v1 mapping)
+#' A data frame of the built-in KRSA kinase coverage file for PamChip
+#' 87102 STK (v1 mapping)
 #'
 #' @format A data frame with 2423 rows and 2 variables:
 #' \describe{
@@ -47,9 +51,11 @@
 #'
 "KRSA_coverage_STK_PamChip_87102_v1"
 
-#' KRSA kinase coverage file for PamChip 87102 STK (v2 mapping, removed PDK kinase)
+#' KRSA kinase coverage file for PamChip 87102 STK (v2 mapping,
+#' removed PDK kinase)
 #'
-#' A data frame of the built-in KRSA kinase coverage file for PamChip 87102 STK (v2 mapping)
+#' A data frame of the built-in KRSA kinase coverage file for
+#' PamChip 87102 STK (v2 mapping)
 #'
 #' @format A data frame with 2423 rows and 2 variables:
 #' \describe{
@@ -62,20 +68,23 @@
 
 #' Protein-Protein Interactions based on PhosphositePlus database
 #'
-#' A data frame of the known Protein-Protein Interactions based on PhosphositePlus database
+#' A data frame of the known Protein-Protein Interactions based on
+#' PhosphositePlus database
 #'
 #' @format A data frame with 179 rows and 2 variables:
 #' \describe{
 #'   \item{FinName}{Kinase Family Name}
-#'   \item{count}{Number of collapsed kinases under that kinase family, it's not used in package}
+#'   \item{count}{Number of collapsed kinases under that kinase family,
+#' it's not used in package}
 #' }
 #'
 "ballModel_nodes"
 
 
 #' Protein-Protein Interactions based on PhosphositePlus database
 #'
-#' A data frame of the known Protein-Protein Interactions based on PhosphositePlus database
+#' A data frame of the known Protein-Protein Interactions based on
+#' PhosphositePlus database
 #'
 #' @format A data frame with 592 rows and 2 variables:
 #' \describe{
@@ -87,7 +96,8 @@
 
 #' CDRL Complete mapping of peptides to HGNC symbols (STK PamChip 87102)
 #'
-#' A data frame of CDRL Complete mapping CDRL Complete mapping of peptides to HGNC symbols (STK PamChip 87102)
+#' A data frame of CDRL Complete mapping CDRL Complete mapping of peptides
+#' to HGNC symbols (STK PamChip 87102)
 #'
 #' @format A data frame with 141 rows and 2 variables:
 #' \describe{
@@ -97,7 +107,8 @@
 
 #' CDRL Complete mapping of peptides to HGNC symbols (PTK PamChip 86402)
 #'
-#' A data frame of CDRL Complete mapping CDRL Complete mapping of peptides to HGNC symbols (PTK PamChip 86402)
+#' A data frame of CDRL Complete mapping CDRL Complete mapping of peptides to
+#' HGNC symbols (PTK PamChip 86402)
 #'
 #' @format A data frame with 193 rows and 2 variables:
 #' \describe{

R/enrichr_lib_call.R

@@ -1,6 +1,8 @@
 #' Runs enrichr api (single GET call for a geneset library)
 #'
-#' This function takes in the geneset library name from Enrichr and userListId (id created by enrichr api) sand retruns tidy dataframe of all geneset terms in that library
+#' This function takes in the geneset library name from Enrichr and
+#' userListId (id created by enrichr api) sand retruns tidy dataframe of
+#' all geneset terms in that library
 #'
 #' @param lib geneset library name from Enrichr
 #' @param userListId id created by the POST enrichr api call
@@ -14,36 +16,38 @@
 #'
 #' @examples
 #' TRUE
-
-
 enrichr_lib_call <- function(lib, userListId) {
-
-  ENRICHR_URL = 'https://maayanlab.cloud/Enrichr/enrich'
-  query_string = '?userListId=%s&backgroundType=%s'
+    ENRICHR_URL <- "https://maayanlab.cloud/Enrichr/enrich"
+    query_string <- "?userListId=%s&backgroundType=%s"
 
 
-  full_link <- base::paste0(ENRICHR_URL,
-                      "?userListId=",
-                      userListId,
-                      "&backgroundType=",
-                      lib)
+    full_link <- base::paste0(
+        ENRICHR_URL,
+        "?userListId=",
+        userListId,
+        "&backgroundType=",
+        lib
+    )
 
-  base::message(base::paste0(lib, " ..."))
+    base::message(base::paste0(lib, " ..."))
 
-  res <- base::suppressMessages(jsonlite::fromJSON(httr::content(httr::GET(full_link), as="text")))
-
-  purrr::map(res[[1]], process_output) %>%
-    purrr::map_df(dplyr::bind_rows) %>%
-    dplyr::mutate(lib = lib)
+    res <- base::suppressMessages(jsonlite::fromJSON(httr::content(
+        httr::GET(full_link),
+        as = "text"
+    )))
 
+    purrr::map(res[[1]], process_output) %>%
+        purrr::map_df(dplyr::bind_rows) %>%
+        dplyr::mutate(lib = lib)
 }
 
 process_output <- function(x) {
-  x <- stats::setNames(x, c("index", "term", "pvalue", "odds_ratio", "combined_score",
-                     "genes", "adjusted_pvalue", "old1", "old2"))
-
-  x[["genes"]] <- base::paste0(x[["genes"]], collapse = ", ")
+    x <- stats::setNames(x, c(
+        "index", "term", "pvalue", "odds_ratio", "combined_score",
+        "genes", "adjusted_pvalue", "old1", "old2"
+    ))
 
-  x
+    x[["genes"]] <- base::paste0(x[["genes"]], collapse = ", ")
 
+    x
 }

R/krsa.R

@@ -17,32 +17,32 @@
 #'
 #' @examples
 #' TRUE
-
-
 krsa <- function(peptides, itr = 2000, seed = 123, return_count = F, map_file = KRSA_file, cov_file = chipCov) {
-  message("Running KRSA ...")
-  set.seed(seed)
-
-  purrr::map_df(1:itr,krsa_sampling,cov_file ,map_file,length(peptides)) -> temp
-
-  temp %>%
-    dplyr::group_by(Kin) %>%
-    dplyr::summarise(SamplingAvg = mean(counts), SD= stats::sd(counts)) -> temp2
-
-  cov_file %>%
-    dplyr::group_by(Kin) %>%
-    dplyr::summarise(
-      Observed = sum(Substrates %in% peptides)
-    ) -> temp3
-
-  dplyr::left_join(temp2, temp3) %>%
-    dplyr::mutate(Z = (Observed-SamplingAvg)/SD) %>%
-    dplyr::arrange(dplyr::desc(abs(Z))) %>%
-    dplyr::filter(!Kin %in% c("BARK1", "VRK2")) %>%
-    dplyr::select(Kin, Observed, SamplingAvg, SD, Z) %>%
-    dplyr::rename(Kinase = Kin) -> fin
-
-  if(return_count == T) {return(list(count_mtx = temp, KRSA_Table = fin))}
-  else {fin}
-
+    message("Running KRSA ...")
+    set.seed(seed)
+
+    purrr::map_df(1:itr, krsa_sampling, cov_file, map_file, length(peptides)) -> temp
+
+    temp %>%
+        dplyr::group_by(Kin) %>%
+        dplyr::summarise(SamplingAvg = mean(counts), SD = stats::sd(counts)) -> temp2
+
+    cov_file %>%
+        dplyr::group_by(Kin) %>%
+        dplyr::summarise(
+            Observed = sum(Substrates %in% peptides)
+        ) -> temp3
+
+    dplyr::left_join(temp2, temp3) %>%
+        dplyr::mutate(Z = (Observed - SamplingAvg) / SD) %>%
+        dplyr::arrange(dplyr::desc(abs(Z))) %>%
+        dplyr::filter(!Kin %in% c("BARK1", "VRK2")) %>%
+        dplyr::select(Kin, Observed, SamplingAvg, SD, Z) %>%
+        dplyr::rename(Kinase = Kin) -> fin
+
+    if (return_count == T) {
+        return(list(count_mtx = temp, KRSA_Table = fin))
+    } else {
+        fin
+    }
 }