M3DropExpressionHeatmap {M3Drop} | R Documentation |
Plots a customized heatmap of scaled log expression values.
M3DropExpressionHeatmap(genes, expr_mat, cell_labels=NA, interesting_genes=NA, key_genes=genes, key_cells=NA)
genes |
a character vector of gene names to be plot. |
expr_mat |
a numeric matrix of normalized (not log-transformed) expression values, columns = samples, rows = genes. |
cell_labels |
factor of labels for each cell in the expression matrix that will be used to coloured in a top bar of the heatmap. |
interesting_genes |
list of vectors of gene names that will be used to colour the bar to the left of the heatmap. |
key_genes |
a character vector of gene names to be labelled on the heatmap. |
key_cells |
a character vector of cells to be labelled on the heatmap. Unlabelled cells will be assigned a numerical index |
Modifies the gplots function heatmap.2 to replace the row dendrogram with a legend of the colours used in the columns colour bar (cell_labels) and use a custom colour scalling. Expression is displayed as Z-scores of log transformed expression (adding a pseudocount of 1) coloured blue-white-red centered at 0 and binned in the range [-2,2].
Invisibly, output from heatmap.2 call.
library(M3DExampleData) M3DropExpressionHeatmap(head(rownames(Mmus_example_list$data),20),Mmus_example_list$data, cell_labels = Mmus_example_list$labels)