Fixed sce path_file bug in seurat trajectory

NBISweden · Feb 15, 2024 · 14c6491 · 14c6491
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diff --git a/compiled/labs/seurat/seurat_07_trajectory.qmd b/compiled/labs/seurat/seurat_07_trajectory.qmd
@@ -359,28 +359,30 @@ Fitting the model:
 >
 > This is a slow compute intensive step, we will not run this now and
 > instead use a pre-computed file in the step below.
->
-> ``` {r}
-> path_file <- "data/trajectory/seurat_scegam.rds"
->
-> # fetch_data is defined at the top of this document
-> if (!fetch_data) {
->   sceGAM <- fitGAM(
->     counts = drop0(obj@assays$RNA@data[sel_genes, sel_cells]),
->     pseudotime = pseudotime[sel_cells, ],
->     cellWeights = cellWeights[sel_cells, ],
->     nknots = 5, verbose = T, parallel = T, sce = TRUE,
->     BPPARAM = BiocParallel::MulticoreParam()
->   )
->   saveRDS(sceGAM, path_file)
-> }
-> ```
 
 </div>
 
+``` {r}
+path_file <- "data/trajectory/seurat_scegam.rds"
+
+# fetch_data is defined at the top of this document
+if (!fetch_data) {
+  sceGAM <- fitGAM(
+    counts = drop0(obj@assays$RNA@data[sel_genes, sel_cells]),
+    pseudotime = pseudotime[sel_cells, ],
+    cellWeights = cellWeights[sel_cells, ],
+    nknots = 5, verbose = T, parallel = T, sce = TRUE,
+    BPPARAM = BiocParallel::MulticoreParam()
+  )
+  saveRDS(sceGAM, path_file)
+}
+```
+
 Download the precomputed file.
 
 ``` {r}
+path_file <- "data/trajectory/seurat_scegam.rds"
+
 # fetch_data is defined at the top of this document
 if (fetch_data) {
   if (!file.exists(path_file)) download.file(url = file.path(path_data, "trajectory/results/seurat_scegam.rds"), destfile = path_file)

diff --git a/docs/labs/index.html b/docs/labs/index.html
@@ -261,7 +261,7 @@ <h1 class="title">Labs</h1>
 <h2 class="anchored" data-anchor-id="fa-brands-r-project-seurat"><i class="fa-brands fa-r-project" aria-label="r-project"></i> Seurat</h2>
 <div id="listing-seurat" class="quarto-listing quarto-listing-container-grid">
 <div class="list grid quarto-listing-cols-4">
-<div class="g-col-1" data-index="0" data-listing-file-modified-sort="1707094565235" data-listing-reading-time-sort="7">
+<div class="g-col-1" data-index="0" data-listing-file-modified-sort="1707212755423" data-listing-reading-time-sort="7">
 <a href="../labs/seurat/seurat_01_qc.html" class="quarto-grid-link">
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@@ -275,7 +275,7 @@ <h5 class="no-anchor card-title listing-title">
 </div>
 </a>
 </div>
-<div class="g-col-1" data-index="1" data-listing-file-modified-sort="1707094565235" data-listing-reading-time-sort="5">
+<div class="g-col-1" data-index="1" data-listing-file-modified-sort="1707212755423" data-listing-reading-time-sort="5">
 <a href="../labs/seurat/seurat_02_dimred.html" class="quarto-grid-link">
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+<div class="g-col-1" data-index="2" data-listing-file-modified-sort="1707598703693" data-listing-reading-time-sort="7">
 <a href="../labs/seurat/seurat_03_integration.html" class="quarto-grid-link">
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+<div class="g-col-1" data-index="3" data-listing-file-modified-sort="1707598703694" data-listing-reading-time-sort="4">
 <a href="../labs/seurat/seurat_04_clustering.html" class="quarto-grid-link">
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@@ -317,7 +317,7 @@ <h5 class="no-anchor card-title listing-title">
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+<div class="g-col-1" data-index="4" data-listing-file-modified-sort="1707250431015" data-listing-reading-time-sort="14">
 <a href="../labs/seurat/seurat_05_dge.html" class="quarto-grid-link">
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-<div class="g-col-1" data-index="5" data-listing-file-modified-sort="1707094565235" data-listing-reading-time-sort="6">
+<div class="g-col-1" data-index="5" data-listing-file-modified-sort="1707250431017" data-listing-reading-time-sort="7">
 <a href="../labs/seurat/seurat_06_celltyping.html" class="quarto-grid-link">
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@@ -345,7 +345,7 @@ <h5 class="no-anchor card-title listing-title">
 </div>
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-<div class="g-col-1" data-index="6" data-listing-file-modified-sort="1707094565235" data-listing-reading-time-sort="13">
+<div class="g-col-1" data-index="6" data-listing-file-modified-sort="1708008688069" data-listing-reading-time-sort="13">
 <a href="../labs/seurat/seurat_07_trajectory.html" class="quarto-grid-link">
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@@ -359,7 +359,7 @@ <h5 class="no-anchor card-title listing-title">
 </div>
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-<div class="g-col-1" data-index="7" data-listing-file-modified-sort="1707175198241" data-listing-reading-time-sort="10">
+<div class="g-col-1" data-index="7" data-listing-file-modified-sort="1707212755427" data-listing-reading-time-sort="10">
 <a href="../labs/seurat/seurat_08_spatial.html" class="quarto-grid-link">
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@@ -383,7 +383,7 @@ <h5 class="no-anchor card-title listing-title">
 <h2 class="anchored" data-anchor-id="fa-brands-r-project-bioconductor"><i class="fa-brands fa-r-project" aria-label="r-project"></i> Bioconductor</h2>
 <div id="listing-bioconductor" class="quarto-listing quarto-listing-container-grid">
 <div class="list grid quarto-listing-cols-4">
-<div class="g-col-1" data-index="0" data-listing-file-modified-sort="1707094565231" data-listing-reading-time-sort="8">
+<div class="g-col-1" data-index="0" data-listing-file-modified-sort="1707212755403" data-listing-reading-time-sort="8">
 <a href="../labs/bioc/bioc_01_qc.html" class="quarto-grid-link">
 <div class="quarto-grid-item card h-100 card-left">
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@@ -397,7 +397,7 @@ <h5 class="no-anchor card-title listing-title">
 </div>
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-<div class="g-col-1" data-index="1" data-listing-file-modified-sort="1707137388623" data-listing-reading-time-sort="5">
+<div class="g-col-1" data-index="1" data-listing-file-modified-sort="1707212755405" data-listing-reading-time-sort="5">
 <a href="../labs/bioc/bioc_02_dimred.html" class="quarto-grid-link">
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-<div class="g-col-1" data-index="2" data-listing-file-modified-sort="1707137402503" data-listing-reading-time-sort="5">
+<div class="g-col-1" data-index="2" data-listing-file-modified-sort="1707598703693" data-listing-reading-time-sort="5">
 <a href="../labs/bioc/bioc_03_integration.html" class="quarto-grid-link">
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-<div class="g-col-1" data-index="3" data-listing-file-modified-sort="1707137395359" data-listing-reading-time-sort="4">
+<div class="g-col-1" data-index="3" data-listing-file-modified-sort="1707212755409" data-listing-reading-time-sort="4">
 <a href="../labs/bioc/bioc_04_clustering.html" class="quarto-grid-link">
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 </div>
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+<div class="g-col-1" data-index="4" data-listing-file-modified-sort="1707212755411" data-listing-reading-time-sort="5">
 <a href="../labs/bioc/bioc_05_dge.html" class="quarto-grid-link">
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@@ -453,7 +453,7 @@ <h5 class="no-anchor card-title listing-title">
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-<div class="g-col-1" data-index="5" data-listing-file-modified-sort="1707137418579" data-listing-reading-time-sort="8">
+<div class="g-col-1" data-index="5" data-listing-file-modified-sort="1707212755412" data-listing-reading-time-sort="8">
 <a href="../labs/bioc/bioc_06_celltyping.html" class="quarto-grid-link">
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@@ -467,7 +467,7 @@ <h5 class="no-anchor card-title listing-title">
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-<div class="g-col-1" data-index="6" data-listing-file-modified-sort="1707094565235" data-listing-reading-time-sort="13">
+<div class="g-col-1" data-index="6" data-listing-file-modified-sort="1707212755416" data-listing-reading-time-sort="13">
 <a href="../labs/bioc/bioc_08_spatial.html" class="quarto-grid-link">
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@@ -491,7 +491,7 @@ <h5 class="no-anchor card-title listing-title">
 <h2 class="anchored" data-anchor-id="fa-brands-python-scanpy"><i class="fa-brands fa-python" aria-label="python"></i> Scanpy</h2>
 <div id="listing-scanpy" class="quarto-listing quarto-listing-container-grid">
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-<div class="g-col-1" data-index="0" data-listing-file-modified-sort="1707094565235" data-listing-reading-time-sort="7">
+<div class="g-col-1" data-index="0" data-listing-file-modified-sort="1707212755419" data-listing-reading-time-sort="7">
 <a href="../labs/scanpy/scanpy_01_qc.html" class="quarto-grid-link">
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-<div class="g-col-1" data-index="1" data-listing-file-modified-sort="1707154848252" data-listing-reading-time-sort="4">
+<div class="g-col-1" data-index="1" data-listing-file-modified-sort="1707212755419" data-listing-reading-time-sort="4">
 <a href="../labs/scanpy/scanpy_02_dimred.html" class="quarto-grid-link">
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+<div class="g-col-1" data-index="2" data-listing-file-modified-sort="1707212755419" data-listing-reading-time-sort="5">
 <a href="../labs/scanpy/scanpy_03_integration.html" class="quarto-grid-link">
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+<div class="g-col-1" data-index="3" data-listing-file-modified-sort="1707212755420" data-listing-reading-time-sort="4">
 <a href="../labs/scanpy/scanpy_04_clustering.html" class="quarto-grid-link">
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+<div class="g-col-1" data-index="4" data-listing-file-modified-sort="1707212755420" data-listing-reading-time-sort="7">
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+<div class="g-col-1" data-index="5" data-listing-file-modified-sort="1707212755421" data-listing-reading-time-sort="6">
 <a href="../labs/scanpy/scanpy_06_celltyping.html" class="quarto-grid-link">
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+<div class="g-col-1" data-index="6" data-listing-file-modified-sort="1707212755421" data-listing-reading-time-sort="8">
 <a href="../labs/scanpy/scanpy_07_trajectory.html" class="quarto-grid-link">
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 </footer>
-<script>var lightboxQuarto = GLightbox({"selector":".lightbox","descPosition":"bottom","openEffect":"zoom","loop":true,"closeEffect":"zoom"});</script>
+<script>var lightboxQuarto = GLightbox({"selector":".lightbox","descPosition":"bottom","openEffect":"zoom","closeEffect":"zoom","loop":true});</script>
 
 
 

diff --git a/docs/labs/seurat/seurat_07_trajectory.html b/docs/labs/seurat/seurat_07_trajectory.html
diff --git a/docs/labs/seurat/seurat_07_trajectory_files/figure-html/unnamed-chunk-21-1.png b/docs/labs/seurat/seurat_07_trajectory_files/figure-html/unnamed-chunk-21-1.png
diff --git a/docs/labs/seurat/seurat_07_trajectory_files/figure-html/unnamed-chunk-23-1.png b/docs/labs/seurat/seurat_07_trajectory_files/figure-html/unnamed-chunk-23-1.png
diff --git a/docs/labs/seurat/seurat_07_trajectory_files/figure-html/unnamed-chunk-25-1.png b/docs/labs/seurat/seurat_07_trajectory_files/figure-html/unnamed-chunk-25-1.png
diff --git a/labs/seurat/seurat_07_trajectory.qmd b/labs/seurat/seurat_07_trajectory.qmd
@@ -295,6 +295,8 @@ Fitting the model:
 
 This is a slow compute intensive step, we will not run this now and instead use a pre-computed file in the step below.
 
+:::
+
 ```{r}
 path_file <- "data/trajectory/seurat_scegam.rds"
 
@@ -311,11 +313,11 @@ if (!fetch_data) {
 }
 ```
 
-:::
-
 Download the precomputed file.
 
 ```{r}
+path_file <- "data/trajectory/seurat_scegam.rds"
+
 # fetch_data is defined at the top of this document
 if (fetch_data) {
   if (!file.exists(path_file)) download.file(url = file.path(path_data, "trajectory/results/seurat_scegam.rds"), destfile = path_file)