Description Usage Arguments Value Author(s) Examples
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.
1 | plotHeatmap(peakdet, exprmat, clustermembers = c())
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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
1 2 3 4 5 6 7 8 9 10 11 12 | # 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]])
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