DoHeatmap: Gene expression heatmap

In nukappa/seurat_v2: Seurat : R toolkit for single cell genomics

Description

Draws a heatmap of single cell gene expression using the heatmap.2 function.

Usage

DoHeatmap(object, cells.use = NULL, genes.use = NULL, disp.min = -2.5,
  disp.max = 2.5, draw.line = TRUE, do.return = FALSE,
  order.by.ident = TRUE, col.use = pyCols, slim.col.label = FALSE,
  group.by = NULL, remove.key = FALSE, cex.col = NULL, do.scale = TRUE,
  ...)

Arguments

object	Seurat object
cells.use	Cells to include in the heatmap (default is all cells)
genes.use	Genes to include in the heatmap (ordered)
disp.min	Minimum display value (all values below are clipped)
disp.max	Maximum display value (all values above are clipped)
draw.line	Draw vertical lines delineating cells in different identity classes.
do.return	Default is FALSE. If TRUE, return a matrix of scaled values which would be passed to heatmap.2
order.by.ident	Order cells in the heatmap by identity class (default is TRUE). If FALSE, cells are ordered based on their order in cells.use
col.use	Color palette to use
slim.col.label	if (order.by.ident==TRUE) then instead of displaying every cell name on the heatmap, display only the identity class name once for each group
group.by	If (order.by.ident==TRUE) default, you can group cells in different ways (for example, orig.ident)
remove.key	Removes the color key from the plot.
cex.col	positive numbers, used as cex.axis in for the column axis labeling. The defaults currently only use number of columns
do.scale	whether to use the data or scaled data
...	Additional parameters to heatmap.2. Common examples are cexRow and cexCol, which set row and column text sizes

Value

If do.return==TRUE, a matrix of scaled values which would be passed to heatmap.2. Otherwise, no return value, only a graphical output

nukappa/seurat_v2 documentation built on May 24, 2019, 9:57 a.m.