plotDEGeneHeatmap: Plot gene heatmap from a SummarizedExperiment object with DE...

In RCPA: Consensus Pathway Analysis

Plot gene heatmap from a SummarizedExperiment object with DE analysis results

Description

Plot gene heatmap from a SummarizedExperiment object with DE analysis results. The heatmap contains p-values and log fold changes from the DE analysis.

Usage

plotDEGeneHeatmap(
  DEResults,
  genes,
  useFDR = TRUE,
  labels = NULL,
  logFCLims = c(-5, 5),
  negLog10pValueLims = c(0, 5)
)

Arguments

DEResults	A named list of data frame of DE analysis results.
genes	A vector of gene id (e.g. Entrez IDs) to plot. The genes must be in the ID column of the data frame in DEResults.
useFDR	If TRUE, use FDR adjusted p-values. Otherwise, use raw p-values.
labels	A vector of labels for the genes. If not provided, the gene IDs will be used as labels.
logFCLims	A vector of length 2 specifying the minimum and maximum log fold change to plot.
negLog10pValueLims	A vector of length 2 specifying the minimum and maximum -log10(p-value) to plot.

Value

A heatmap of the genes from ggplot2.

Examples

library(RCPA)
library(SummarizedExperiment)

affyDEExperiment <- loadData("affyDEExperiment")
agilDEExperiment <- loadData("agilDEExperiment")
RNASeqDEExperiment <- loadData("RNASeqDEExperiment")
metaDEResult <- loadData("metaDEResult")
genesets <- loadData("genesets")

DEResults <- list(
    "Affymetrix - GSE5281" = rowData(affyDEExperiment),
    "Agilent - GSE61196" = rowData(agilDEExperiment),
    "RNASeq - GSE153873" = rowData(RNASeqDEExperiment)
)

 metaDEResult <- metaDEResult[order(metaDEResult$pFDR),]

 alzheimerGenes <- genesets$genesets[["path:hsa05010"]]
 genesToPlot <- head(metaDEResult[metaDEResult$ID %in% alzheimerGenes, ], 50)$ID

 genesAnnotation <- RCPA::getEntrezAnnotation(genesToPlot)
 labels <- genesAnnotation[genesToPlot, "Description"]

 genesOrderByFC <- order(metaDEResult[match(genesToPlot, metaDEResult$ID), "logFC"])
 resultsToPlot <- c(DEResults, list(metaDEResult))
 names(resultsToPlot) <- c(names(DEResults), "Meta-analysis")

 plotObj <- RCPA::plotDEGeneHeatmap(
     resultsToPlot,
     genesToPlot[genesOrderByFC],
     labels = labels[genesOrderByFC],
     negLog10pValueLims = c(0, 5), logFCLims = c(-1, 1)
 )

RCPA documentation built on Nov. 21, 2023, 5:08 p.m.