Improved QC Reports - June 2020 (NW)

[wong-nw]

Changes pushed June 2020

scrnaQC.R Catch for only importing reads in event of multi-assay h5 file Saving npcs as metadata in misc array QC Image outputs at end of script:

• List of statistics
• Venn diagram
• Violins pre- and post-filter
• Cluster UMAPs and silhouettes
• Pre-doublet filter UMAP
• Cell cycle UMAP
• QC images for all annotations datasets

Save seurat object pre-doublet removal Remove saving of full Rdata workspaces

scrnaQC.snakefile Include new files produced as input/output for rule all, rule qc_scrna, rule qcReport_scrna. All pdf/png images used to generate QC report. Modified qcReport_scrna to call expanded scrnaQC_Report.R

scrnaQC_Report.R Added parameters to scrnaQC.Rmd call:

• Output file name
• Output file directory (QC)
• Parameters: Image storage directory, resolution list, sample ID

scrnaQC.Rmd Full re-write of Rmd file to only grab images New images included described above

integrateBatches.R Cleaned up old calls across multiple clustering resolutions

[skchronicles]

Thanks @wong-nw, everything looks good!