Seurat (version 2.1.0)

OldDoHeatmap: Gene expression heatmap

Description

Draws a heatmap of single cell gene expression using the heatmap.2 function. Has been replaced by the ggplot2 version (now in DoHeatmap), but kept for legacy

Usage

OldDoHeatmap(object, cells.use = NULL, genes.use = NULL, disp.min = NULL,
  disp.max = NULL, draw.line = TRUE, do.return = FALSE,
  order.by.ident = TRUE, col.use = PurpleAndYellow(),
  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

Examples

# NOT RUN {
pbmc_small
OldDoHeatmap(object = pbmc_small, genes.use = [e-mail])

# }