plotHeatmap {Biopeak} | R Documentation |
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.
plotHeatmap(peakdet, exprmat, clustermembers = c())
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. |
This function does not return any value but generates a heatmap plot.
David Lauenstein
# 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]])