plotMutInteract {pathwayTMB}

Exact tests to detect mutually exclusive, co-occuring and altered genesets or pathways.

Description

Performs Pair-wise Fisher's Exact test to detect mutually exclusive or co-occuring events.

Usage

plotMutInteract(
  freq_matrix,
  genes,
  pvalue = c(0.05, 0.01),
  returnAll = TRUE,
  fontSize = 0.8,
  showSigSymbols = TRUE,
  showCounts = FALSE,
  countStats = "all",
  countType = "all",
  countsFontSize = 0.8,
  countsFontColor = "black",
  colPal = "BrBG",
  nShiftSymbols = 5,
  sigSymbolsSize = 2,
  sigSymbolsFontSize = 0.9,
  pvSymbols = c(46, 42),
  limitColorBreaks = TRUE
)

Arguments

freq_matrix

The mutations matrix,generated by 'get_mut_matrix'.

genes

List of genes or pathways among which interactions should be tested.

pvalue

Default c(0.05, 0.01) p-value threshold. You can provide two values for upper and lower threshold.

returnAll

If TRUE returns test statistics for all pair of tested genes. Default FALSE, returns for only genes below pvalue threshold.

fontSize

cex for gene names. Default 0.8.

showSigSymbols

Default TRUE. Heighlight significant pairs.

showCounts

Default TRUE. Include number of events in the plot.

countStats

Default 'all'. Can be 'all' or 'sig'.

countType

Default 'cooccur'. Can be 'all', 'cooccur', 'mutexcl'.

countsFontSize

Default 0.8.

countsFontColor

Default 'black'.

colPal

colPalBrewer palettes. See RColorBrewer::display.brewer.all() for details.

nShiftSymbols

shift if positive shift SigSymbols by n to the left, default = 5.

sigSymbolsSize

size of symbols in the matrix and in legend.

sigSymbolsFontSize

size of font in legends.

pvSymbols

vector of pch numbers for symbols of p-value for upper and lower thresholds c(upper, lower).

limitColorBreaks

limit color to extreme values. Default TRUE.

Value

list of data.tables

Examples

#get the path of the mutation annotation file and samples' survival data
maf<-system.file("extdata","data_mutations_extended.txt",package = "pathwayTMB")
sur_path<-system.file("extdata","sur.csv",package = "pathwayTMB")
sur<-read.csv(sur_path,header=TRUE,row.names = 1)
#perform the function 'get_mut_matrix'
mut_matrix<-get_mut_matrix(maffile=maf,mut_fre = 0.01,is.TCGA=FALSE,sur=sur)
#perform the function `get_PTMB`
PTMB_matrix<-get_PTMB(freq_matrix=mut_matrix,genesmbol=genesmbol,gene_path=gene_path)
set.seed(1)
final_character<-get_final_signature(PTMB=PTMB_matrix,sur=sur)
plotMutInteract(freq_matrix=PTMB_matrix, genes=final_character,nShiftSymbols =0.3)