Attempt to identify tumor cells in those non-ETP samples without B cells (SCPCP000003)

.github/workflows/run_cell-type-nonETP-ALL-03.yml

@@ -89,4 +89,5 @@ jobs:
           # run module script(s) here
           Rscript scripts/00-01_processing_rds.R
           Rscript scripts/02-03_annotation.R
-          Rscript scripts/multipanel_plot.R
+          Rscript scripts/04_multipanel_plot.R
+          Rscript scripts/05_cluster_evaluation.R

analyses/cell-type-nonETP-ALL-03/renv.lock

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@@ -1083,6 +1145,32 @@
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@@ -1560,6 +1742,24 @@
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@@ -1748,6 +1948,17 @@
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@@ -1899,6 +2110,30 @@
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analyses/cell-type-nonETP-ALL-03/results/README.md

@@ -12,4 +12,8 @@ These are the generated outputs for each sample in the S3 bucket:
 -   `rds` objects: `s3://researcher-650251722463-us-east-2/cell-type-nonETP-ALL-03/results/rds`
 -   metadata and ScType results: `s3://researcher-650251722463-us-east-2/cell-type-nonETP-ALL-03/results/`
 -   CopyKat results: `s3://researcher-650251722463-us-east-2/cell-type-nonETP-ALL-03/results/copykat_output`
--   umap and dot plots: `s3://researcher-650251722463-us-east-2/cell-type-nonETP-ALL-03/plots` (are also found in the repository plots/).
+-   evaluating cluster separation, stability, and purity: `s3://researcher-650251722463-us-east-2/cell-type-nonETP-ALL-03/results/evalClus`
+-   umap and dot plots: `s3://researcher-650251722463-us-east-2/cell-type-nonETP-ALL-03/plots`
+-   violin and stacked bar plots for exploring the results of CopyKat prediction: `s3://researcher-650251722463-us-east-2/cell-type-nonETP-ALL-03/plots/copykat_exploration`
+
+\*\*All the plots are also found in the repository plots/.