Create readme.md

scSNViz/readme.md

@@ -0,0 +1,42 @@
+# snv\_plotter_tsne.r (Updated: 05/14/2024)
+# snv\_plotter_pca.r (Updated: 05/14/2024)
+# snv\_plotter_umap.r (Updated: 05/14/2024)
+## Introduction
+snv\_plotter_tsne\/pca\/umap.r scripts plot information about SNVs provided by the user onto a
+dimensionally reduced representation of the data (either tsne, pca, or umap,
+depending on the script selected). Currently, the script generates a set of 
+plots that represent basic statistics and properties of the SNVs identified
+in the dataset and utilize existing packages, such as Seurat, Slingshot, and scType.
+
+## Input
+The script accepts three inputs:
+- STAR solo output directory (-m) that contains features.tsv.gz, barcodes.tsv.gz, and matrix.mtx.gz OR a Seurat object (-r) that was saved as a .RDS
+- SCReadCounts output file (-t) that is tab-delimited and either a .tsv or .txt
+
+See sample files for reference.
+
+## Output
+The produced figures include:
+- Histogram of mean VAF per SNV per cell
+- Histogram of the number of SNVs per cell
+- Histogram of the number of Variant Reads per cell
+- Histogram of the Total VAF per cell (VARreads/(VARreads+REFreads) per cell)
+
+- 3D UMAP representation of mean VAF for each cell
+- 3D UMAP representation of median VAF for each cell
+- 3D UMAP representation of number of number of SNVs for each cell
+- 3D UMAP representation of number of Variant Reads for each cell
+- 3D UMAP representation of number of Reference Reads for each cell
+- 3D UMAP representation of Total VAF per cell (VARreads/(VARreads+REFreads) per cell)
+
+- Individual SNV plots
+  - VAF per cell
+  - Number of Reference Reads per cell
+  - Number of Variant Reads per cell
+
+## Examples
+ml R
+
+Rscript 240508_multivar_plotter_tsne_blRed.r -t SNV_file.txt -m SAMNXX_wasp_Solo.out/Gene/filtered/
+
+Rscript 240508_multivar_plotter_tsne_blRed.r -t SNV_file.txt -m SAMNXX_wasp_Solo.out/Gene/filtered/ --th-vars=1 --th-reads=10 --tissue-type=Liver -c -d -e