PICTographPlus_manuscript

Scripts used for generating results in the PICTographPlus manuscript

Scripts used for Benchmarking

GSE155698.R is used for the following:

• generate inferCNV results
• build copy number tree
• run simulations

1. To run inferCNV and build copy number trees, first obtain single cell data from GEO accession number GSE155698, PDAC_TISSUE_8, then run Rscript GSE155698.R. This will give all_cells_with_hmm.rds and tree.csv files, which will be used for downstream simulation. These two files are also available on Mendeley.

2. To run simulations, use Rscript GSEA155698.R {outputDir} {number of samples} {single cell percentage} {purity} {seed}. The complete list of parameters used for the benchmarking analysis can be found at GSE155698_array_jobs.txt. The collected results are available on Mendeley, and results were visualized using visualization.ipynb.

Scripts used for Results Section

pictographPlus_results.Rmd can be used to generate result section data. The input files are available on Mendeley. Final figures in the manuscript were curated by a professional artist so there is no code for generating the identical figures.