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 Has been replaced by the ggplot2 version (now in DoHeatmap), but kept for legacy
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 = pyCols, slim.col.label = FALSE,
group.by = NULL, remove.key = FALSE, cex.col = NULL, do.scale = TRUE,
...)Seurat object
Cells to include in the heatmap (default is all cells)
Genes to include in the heatmap (ordered)
Minimum display value (all values below are clipped)
Maximum display value (all values above are clipped)
Draw vertical lines delineating cells in different identity classes.
Default is FALSE. If TRUE, return a matrix of scaled values which would be passed to heatmap.2
Order cells in the heatmap by identity class (default is TRUE). If FALSE, cells are ordered based on their order in cells.use
Color palette to use
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
If (order.by.ident==TRUE) default, you can group cells in different ways (for example, orig.ident)
Removes the color key from the plot.
positive numbers, used as cex.axis in for the column axis labeling. The defaults currently only use number of columns
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
If do.return==TRUE, a matrix of scaled values which would be passed to heatmap.2. Otherwise, no return value, only a graphical output