Draws a heatmap of single cell feature expression.
DoHeatmap( object, features = NULL, cells = NULL, group.by = "ident", group.bar = TRUE, group.colors = NULL, disp.min = -2.5, disp.max = NULL, slot = "scale.data", assay = NULL, label = TRUE, size = 5.5, hjust = 0, vjust = 0, angle = 45, raster = TRUE, draw.lines = TRUE, lines.width = NULL, group.bar.height = 0.02, combine = TRUE )
A vector of features to plot, defaults to
VariableFeatures(object = object)
A vector of cells to plot
A vector of variables to group cells by; pass 'ident' to group by cell identity classes
Add a color bar showing group status for cells
Colors to use for the color bar
Minimum display value (all values below are clipped)
Maximum display value (all values above are clipped); defaults to 2.5
slot is 'scale.data', 6 otherwise
Data slot to use, choose from 'raw.data', 'data', or 'scale.data'
Assay to pull from
Label the cell identies above the color bar
Size of text above color bar
Horizontal justification of text above color bar
Vertical justification of text above color bar
Angle of text above color bar
If true, plot with geom_raster, else use geom_tile. geom_raster may look blurry on some viewing applications such as Preview due to how the raster is interpolated. Set this to FALSE if you are encountering that issue (note that plots may take longer to produce/render).
Include white lines to separate the groups
Integer number to adjust the width of the separating white lines. Corresponds to the number of "cells" between each group.
Scale the height of the color bar
Combine plots into a single
ggplot object. If
FALSE, return a list of ggplot objects
patchworked ggplot object if
combine = TRUE; otherwise, a list of ggplot objects
data("pbmc_small") DoHeatmap(object = pbmc_small)