get_plotMutInteract {ProgModule}

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

get_plotMutInteract(
  module = NULL,
  genes = NULL,
  freq_matrix,
  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

module

The gene module,generated by 'get_final_candidate_module'.

genes

The modular gene,generated by 'get_final_candidate_module'.

freq_matrix

The mutations matrix,generated by 'get_mut_status'.

pvalue, returnAll, fontSize, showSigSymbols, showCounts, countStats, countType, countsFontSize, countsFontColor, colPal, nShiftSymbols, sigSymbolsSize, sigSymbolsFontSize, pvSymbols, limitColorBreaks

see plotMutInteract

Value

No return value

Examples

#load the data.
data(plotMutInteract_moduledata,plotMutInteract_mutdata)
#draw an plotMutInteract of genes
get_plotMutInteract(genes=unique(unlist(plotMutInteract_moduledata)),
freq_matrix=plotMutInteract_mutdata)
#draw an plotMutInteract of modules
get_plotMutInteract(module=plotMutInteract_moduledata,
freq_matrix=plotMutInteract_mutdata)