pictographPlus_results.Rmd

---
title: "pictographPlus"
output: html_document
date: "2025-03-17"
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```

```{r}
library(pictographPlus)
library(DESeq2)
library(IRanges)
```

# run Semaan et al. patient MK74

```{r}
patient ='MK74'
mutation_file = 'MK74_snv.csv'
copy_number_file = 'MK74_cn.csv'
SNV_file = 'MK74_pileup.csv'
outputDir = 'MK74'
suppressWarnings(dir.create(outputDir))

rna_file = paste0(dataDir, patient, '_rna.csv')
GSEA_file="gene_sets_extended.txt"

runPICTographPlus(mutation_file=mutation_file,
                  copy_number_file=copy_number_file,
                  SNV_file = SNV_file,
                  outputDir=outputDir,
                  rna_file = rna_file,
                  GSEA_file=GSEA_file)
```

# run PanCurx patient PCSI0380

```{r}
patient ='PCSI0380'
mutation_file = 'PCSI0380_snv_only.csv'
outputDir = 'PCSI0380'
suppressWarnings(dir.create(outputDir))

rna_file = paste0(dataDir, patient, ".csv")
GSEA_file="gene_sets_extended.txt"

runPICTographPlus(mutation_file=mutation_file,
                  rna_file = rna_file,
                  outputDir=outputDir,
                  GSEA_file=GSEA_file)
```

# run TRACERx patient CRUK0004

```{r}

patient = 'CRUK0004'

mutation_file = 'CRUK0004_SNV.csv'
copy_number_file = 'CRUK0004_facets.csv'
outputDir = 'CRUK0004'
suppressWarnings(dir.create(outputDir))

runPictograph(mutation_file=mutation_file,
              copy_number_file=copy_number_file,
              outputDir=outputDir,
              tcn_normal_range = c(1.7,2.3),
              inits=list(".RNG.name" = "base::Wichmann-Hill",".RNG.seed" = 111))

rna_file = paste0(dataDir, patient, '_RNA.csv')

GSEA_file="gene_sets_extended.txt"
treeFile = paste(outputDir, "tree.csv", sep="/")
proportionFile = paste(outputDir, "subclone_proportion.csv", sep="/")

X_optimal = runDeconvolution(rna_file = rna_file,
              treeFile = treeFile,
              proportionFile = proportionFile,
              outputDir = outputDir)

runGSEA(X_optimal, outputDir, treeFile, GSEA_file=GSEA_file)

```