M3D_Expression_Heatmap: Plot Heatmap of Gene Expression
In tallulandrews/M3D: Michaelis-Menten Modelling of Dropouts in single-cell RNASeq

Description Usage Arguments Details Value Examples

Plots a customized heatmap of scaled log expression values. Functions tagged with "bg__" are not meant for direct usage and are not available in the Bioconductor release.

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  M3DropExpressionHeatmap(genes, expr_mat, cell_labels=NA, interesting_genes=NA, key_genes=genes, key_cells=NA)
  bg__expression_heatmap(genes, expr_mat, cell_labels=NA, gene_labels=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 colour the bar on the top 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
`gene_labels`	factor of labels for each gene that will be used to colour the bar on the left of the heatmap.

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].

M3DropExpressionHeatmap is a wrapper for bg__expression_heatmap that checks and reformats provided arguments.

Invisibly, output from heatmap.2 call.

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  library(M3DExampleData)
  M3DropExpressionHeatmap(head(rownames(Mmus_example_list$data),20),Mmus_example_list$data, cell_labels = Mmus_example_list$labels)
#  bg__expression_heatmap(head(rownames(Mmus_example_list$data),20),Mmus_example_list$data, cell_labels = Mmus_example_list$labels)