plotHeatmap: Plot a heatmap for selected genes

In Biopeak: Identification of Impulse-Like Gene Expression Changes in Short Genomic Series Data

Description

This function acts as a wrapper function for the heatmap.2 function of the gplots package and normalizes the subjected expression matrix to the log2 of the mean expression of the gene across all time-points.

Usage

plotHeatmap(peakdet, exprmat, clustermembers = c())

Arguments

peakdet	A list returned by the peakDetection function.
exprmat	A numeric matrix with expression series data with variables as rownames.
clustermembers	An optional character vector defining genes to be selected.

Value

This function does not return any value but generates a heatmap plot.

Author(s)

David Lauenstein

Examples

# Example based on the heat-shock dataset
data(heat)
heat = as.matrix(heat)
# Define series
series <- c(37,40,41,42,43)
# Run the peak detection algorithm
peakdet <- peakDetection(heat, series, type ='rnaseq', actstrength = 1.5,
prominence = 1.3, minexpr = 5000)
# cluster exploration using kmeans with a maximum of 4 clusters to be assigned
clusters <- findClusters(peakdet, heat, maxclusters = 4, method = 'kmeans')
# Plot the heatmap for one of the clusters returned by the findClusters function
heatmap <- plotHeatmap(peakdet, heat, clustermembers = clusters$clustermembers[[1]])

Biopeak documentation built on Aug. 21, 2019, 5:10 p.m.