plotBarChart {RCPA}

Plot a bar chart of the pathway analysis results

Description

This function plots a bar chart of the pathway analysis results.

Usage

plotBarChart(
  results,
  limit = Inf,
  label = "name",
  by = c("normalizedScore", "score", "pFDR", "p.value"),
  maxNegLog10PValue = 5,
  pThreshold = 0.05,
  useFDR = TRUE,
  selectedPathways = NULL
)

Arguments

results

A named list of data frame with pathway analysis results. The columns are ID, name, p.value, pFDR, size, nDE, score and normalizedScore.

limit

The maximum number of pathways to plot. The pathway will be sorted by the average absolute value of the -log10(p-value) or -log10(pFDR) if the 'by' parameter is 'p.value' or 'pFDR'. Otherwise, the pathway will be sorted by the average value of the 'by' parameter.

label

The column to use for the labels.

by

The column to use for the bar heights.

maxNegLog10PValue

The maximum -log10(p-value) to plot.

pThreshold

The p-value threshold to use for significance.

useFDR

If TRUE, use FDR adjusted p-values for the significance threshold. Otherwise, use raw p-values. This parameter is used to mark the color of the bars and is independent of the 'by' parameter.

selectedPathways

A vector of pathways ID, which is in the same format as ID column in the pathway analysis result, to be included in the plot. If it is NULL, all pathways will be included.

Value

A ggplot2 object.

Examples

library(RCPA)

affyFgseaResult <- loadData("affyFgseaResult")
agilFgseaResult <- loadData("agilFgseaResult")
RNASeqFgseaResult <- loadData("RNASeqFgseaResult")
metaPAResult <- loadData("metaPAResult")

PAResults <- list(
    "Affymetrix - GSE5281" = affyFgseaResult,
    "Agilent - GSE61196" = agilFgseaResult,
    "RNASeq - GSE153873" = RNASeqFgseaResult,
    "Meta-analysis" = metaPAResult
)

selectedPathways <- c("path:hsa05010", "path:hsa05012", "path:hsa05014", 
                       "path:hsa05016", "path:hsa05017", "path:hsa05020", 
                       "path:hsa05022", "path:hsa04724", "path:hsa04727", 
                       "path:hsa04725", "path:hsa04728", "path:hsa04726",
                      "path:hsa04720", "path:hsa04730", "path:hsa04723", 
                      "path:hsa04721", "path:hsa04722")
resultsToPlot <- lapply(PAResults, 
                    function(df) df[df$ID %in% selectedPathways,])

plotObj <- RCPA::plotBarChart(resultsToPlot) + 
            ggplot2::ggtitle("FGSEA Analysis Results")