M3DropExpressionHeatmap {M3Drop} | R Documentation

## Plot Heatmap of Gene Expression

### Description

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.

### Usage

      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)

### Arguments

`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.

### Details

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.

### Value

Invisibly, output from heatmap.2 call.

### Examples

      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)

[Package M3Drop version 1.12.0 Index]