Draws a heatmap of single cell gene expression using ggplot2.
DoHeatmap(object, data.use = NULL, use.scaled = TRUE, cells.use = NULL,
genes.use = NULL, disp.min = -2.5, disp.max = 2.5, group.by = "ident",
group.order = NULL, draw.line = TRUE, col.low = "#FF00FF",
col.mid = "#000000", col.high = "#FFFF00", slim.col.label = FALSE,
remove.key = FALSE, rotate.key = FALSE, title = NULL, cex.col = 10,
cex.row = 10, group.label.loc = "bottom", group.label.rot = FALSE,
group.cex = 15, group.spacing = 0.15, assay.type = "RNA",
do.plot = TRUE)Seurat object
Option to pass in data to use in the heatmap. Default will pick from either object@data or object@scale.data depending on use.scaled parameter. Should have cells as columns and genes as rows.
Whether to use the data or scaled data if data.use is NULL
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)
Groups cells by this variable. Default is object@ident
Order of groups from left to right in heatmap.
Draw vertical lines delineating different groups
Color for lowest expression value
Color for mid expression value
Color for highest expression value
display only the identity class name once for each group
Removes the color key from the plot.
Rotate color scale horizantally
Title for plot
Controls size of column labels (cells)
Controls size of row labels (genes)
Place group labels on bottom or top of plot.
Whether to rotate the group label.
Size of group label text
Controls amount of space between columns.
to plot heatmap for (default is RNA)
Whether to display the plot.
Returns a ggplot2 plot object
# NOT RUN {
DoHeatmap(object = pbmc_small)
# }
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