cheatmap: Heatmap for gene expression pattern.
In charliex210/sctools: Tools for single cell RNAseq analysis

Plot the clustering result of cells and genes.

cheatmap(mat, filename = NA, vmax = 2, vmin = -1, log = FALSE,
  scale = FALSE, hlight = NULL, cmap = NULL, cluster_rows = TRUE,
  cluster_cols = TRUE, gene_labels = NULL, cell_labels = NULL,
  gene_order = NULL, cell_order = NULL, gaps_row = NULL,
  gaps_col = NULL, anno_row = NA, anno_col = NA, plot_gaps_row = TRUE,
  plot_gaps_col = TRUE, re_write_gene_labels = FALSE,
  re_write_cell_labels = FALSE, ...)

`mat`	Expression matrix, columns are cells and rows are genes.
`filename`	Filename to save your heatmap.
`vmax`	The maximum value to plot.
`vmin`	The minimum value to plot.
`log`	log2 tranform the data.
`scale`	Scale the data, result in mean = 0 and std = 1 of each gene.
`hlight`	The genes you want to highlight in the heatmap.
`cmap`	The pallette of the heatmap, one can generate it using colorRampPalette().
`cluster_rows`	boolean values determining if rows should be clustered or hclust object.
`cluster_cols`	boolean values determining if columns should be clustered or hclust object.
`gene_labels`	A vector of gene clustering labels.
`cell_labels`	A vector of cell clustering labels.
`gene_order`	Specify a sequence of gene clusters order, the values must be in gene_labels.
`cell_order`	Specify a sequence of cell clusters order, the values must be in cell_labels.
`gaps_row`	A vector indicates gaps of row, if NULL the gaps will be setting based on the gene_labels.
`gaps_col`	A vector indicates gaps of column, if NULL the gaps will be setting based on the cell_labels.
`anno_row`	Data frame that specifies the annotations shown on left side of the heatmap. Each row defines the features for a specific row. The rows in the data and in the annotation are matched using corresponding row names. Note that color schemes takes into account if variable is continuous or discrete.
`anno_col`	Similar to annotation_row, but for columns.
`plot_gaps_row`	Make gaps on row.
`plot_gaps_col`	Make gaps on column.
`re_write_gene_labels`	Re-write gene labels to an ordered sequeence.
`re_write_cell_labels`	Re-write cell labels to an ordered sequeence.
`...`	Additional arguments passed on to pheatmap.