Feature expression heatmap
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, angle = 45, raster = TRUE, draw.lines = TRUE, lines.width = NULL, group.bar.height = 0.02, combine = TRUE )
object |
Seurat object |
features |
A vector of features to plot, defaults to |
cells |
A vector of cells to plot |
group.by |
A vector of variables to group cells by; pass 'ident' to group by cell identity classes |
group.bar |
Add a color bar showing group status for cells |
group.colors |
Colors to use for the color bar |
disp.min |
Minimum display value (all values below are clipped) |
disp.max |
Maximum display value (all values above are clipped); defaults to 2.5
if |
slot |
Data slot to use, choose from 'raw.data', 'data', or 'scale.data' |
assay |
Assay to pull from |
label |
Label the cell identies above the color bar |
size |
Size of text above color bar |
hjust |
Horizontal justification of text above color bar |
angle |
Angle of text above color bar |
raster |
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). |
draw.lines |
Include white lines to separate the groups |
lines.width |
Integer number to adjust the width of the separating white lines. Corresponds to the number of "cells" between each group. |
group.bar.height |
Scale the height of the color bar |
combine |
Combine plots into a single |
A patchworked ggplot object if
combine = TRUE; otherwise, a list of ggplot objects
data("pbmc_small")
DoHeatmap(object = pbmc_small)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.