plotMutInteract: Exact tests to detect mutually exclusive, co-occuring and...
In pathwayTMB: Pathway Based Tumor Mutational Burden

plotMutInteract

R Documentation

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)

pathwayTMB documentation built on Aug. 9, 2022, 5:09 p.m.