Added test code to check dir

_episodes/04-Quality-Control.md

@@ -31,6 +31,29 @@ data_dir <- '../data'
 {: .language-r}
 
 
+~~~
+dir(data_dir)
+~~~
+{: .language-r}
+
+
+
+~~~
+ [1] "lesson03.Rdata"                                
+ [2] "lesson03_challenge.Rdata"                      
+ [3] "lesson04.rds"                                  
+ [4] "lesson05.Rdata"                                
+ [5] "lesson05.rds"                                  
+ [6] "mouseStSt_exvivo"                              
+ [7] "mouseStSt_exvivo.zip"                          
+ [8] "mouseStSt_invivo"                              
+ [9] "mouseStSt_invivo.zip"                          
+[10] "regev_lab_cell_cycle_genes_mm.fixed.txt"       
+[11] "regev_lab_cell_cycle_genes_mm.fixed.txt_README"
+~~~
+{: .output}
+
+
 
 
 <img src="../fig/single_cell_flowchart_0.png" width="800px" alt="Single Cell Flowchart" >
@@ -85,8 +108,8 @@ doublet_preds <- colData(sce)
 
 ~~~
             used   (Mb) gc trigger   (Mb)  max used   (Mb)
-Ncells   8111351  433.2   14166592  756.6  11252362  601.0
-Vcells 181808817 1387.1  436713378 3331.9 436709905 3331.9
+Ncells   8111953  433.3   14168290  756.7  11252398  601.0
+Vcells 181810210 1387.2  436715070 3331.9 436711315 3331.9
 ~~~
 {: .output}
 
@@ -341,8 +364,8 @@ gc()
 
 ~~~
             used   (Mb) gc trigger   (Mb)  max used   (Mb)
-Ncells   8269310  441.7   14166592  756.6  12309993  657.5
-Vcells 182529992 1392.6  596761613 4553.0 629553055 4803.2
+Ncells   8269380  441.7   14168290  756.7  12310063  657.5
+Vcells 182530194 1392.6  596761865 4553.0 629553222 4803.2
 ~~~
 {: .output}
 

_episodes/05-Common-Analyses.md

@@ -270,7 +270,7 @@ Formal class 'Seurat' [package "SeuratObject"] with 13 slots
   ..@ commands    :List of 2
   .. ..$ NormalizeData.RNA       :Formal class 'SeuratCommand' [package "SeuratObject"] with 5 slots
   .. .. .. ..@ name       : chr "NormalizeData.RNA"
-  .. .. .. ..@ time.stamp : POSIXct[1:1], format: "2024-10-16 01:45:53"
+  .. .. .. ..@ time.stamp : POSIXct[1:1], format: "2024-10-16 02:16:45"
   .. .. .. ..@ assay.used : chr "RNA"
   .. .. .. ..@ call.string: chr "NormalizeData(., normalization.method = \"LogNormalize\")"
   .. .. .. ..@ params     :List of 5
@@ -281,7 +281,7 @@ Formal class 'Seurat' [package "SeuratObject"] with 13 slots
   .. .. .. .. ..$ verbose             : logi TRUE
   .. ..$ FindVariableFeatures.RNA:Formal class 'SeuratCommand' [package "SeuratObject"] with 5 slots
   .. .. .. ..@ name       : chr "FindVariableFeatures.RNA"
-  .. .. .. ..@ time.stamp : POSIXct[1:1], format: "2024-10-16 01:46:01"
+  .. .. .. ..@ time.stamp : POSIXct[1:1], format: "2024-10-16 02:16:53"
   .. .. .. ..@ assay.used : chr "RNA"
   .. .. .. ..@ call.string: chr "FindVariableFeatures(., nfeatures = 2000)"
   .. .. .. ..@ params     :List of 12

_episodes/06-Biology-Driven-Analyses.md

@@ -306,28 +306,28 @@ Computing SNN
 
 
 ~~~
-01:55:19 UMAP embedding parameters a = 0.9922 b = 1.112
+02:26:05 UMAP embedding parameters a = 0.9922 b = 1.112
 ~~~
 {: .output}
 
 
 
 ~~~
-01:55:19 Read 44253 rows and found 24 numeric columns
+02:26:05 Read 44253 rows and found 24 numeric columns
 ~~~
 {: .output}
 
 
 
 ~~~
-01:55:19 Using Annoy for neighbor search, n_neighbors = 30
+02:26:05 Using Annoy for neighbor search, n_neighbors = 30
 ~~~
 {: .output}
 
 
 
 ~~~
-01:55:19 Building Annoy index with metric = cosine, n_trees = 50
+02:26:05 Building Annoy index with metric = cosine, n_trees = 50
 ~~~
 {: .output}
 
@@ -349,13 +349,13 @@ Computing SNN
 
 ~~~
 **************************************************|
-01:55:23 Writing NN index file to temp file C:\Users\c-dgatti\AppData\Local\Temp\RtmpWWaahB\file3260428514ec
-01:55:23 Searching Annoy index using 1 thread, search_k = 3000
-01:55:33 Annoy recall = 100%
-01:55:34 Commencing smooth kNN distance calibration using 1 thread with target n_neighbors = 30
-01:55:37 Initializing from normalized Laplacian + noise (using RSpectra)
-01:55:47 Commencing optimization for 200 epochs, with 1888044 positive edges
-01:56:25 Optimization finished
+02:26:09 Writing NN index file to temp file C:\Users\c-dgatti\AppData\Local\Temp\Rtmpua4Qd7\file2e34780d10a1
+02:26:09 Searching Annoy index using 1 thread, search_k = 3000
+02:26:20 Annoy recall = 100%
+02:26:21 Commencing smooth kNN distance calibration using 1 thread with target n_neighbors = 30
+02:26:24 Initializing from normalized Laplacian + noise (using RSpectra)
+02:26:34 Commencing optimization for 200 epochs, with 1888044 positive edges
+02:27:12 Optimization finished
 ~~~
 {: .output}
 

_episodes_rmd/04-Quality-Control.Rmd

@@ -29,6 +29,10 @@ suppressPackageStartupMessages(library(Seurat))
 data_dir <- '../data'
 ```
 
+```{r test_chunk}
+dir(data_dir)
+```
+
 
 ```{r load_data,include=FALSE}
 # Only needed to build lessons.