do_GroupwiseDEHeatmap() | Differential expression

Groupwise DE heatmaps visualize the results of Seurat::FindAllMarkers() as a multi-panel dot plot showing adjusted p-values, fold changes, and mean expression per cluster.

Basic usage

First run FindAllMarkers():

de_genes <- Seurat::FindAllMarkers(sample, only.pos = TRUE)

p <- SCpubr::do_GroupwiseDEHeatmap(sample = sample,
                                   de_genes = de_genes)
p

Adjust number of top genes

p <- SCpubr::do_GroupwiseDEHeatmap(sample = sample,
                                   de_genes = de_genes,
                                   top_genes = 3)
p

Custom p-value cutoff

p <- SCpubr::do_GroupwiseDEHeatmap(sample = sample,
                                   de_genes = de_genes,
                                   p.cutoff = 0.01)
p

Adjust dot size

p <- SCpubr::do_GroupwiseDEHeatmap(sample = sample,
                                   de_genes = de_genes,
                                   dot.scale = 6)
p

Parameter reference

Note

For parameters shared across many functions (color palettes, typography, legend styling), see Shared features.

Core parameters

Parameter Description Default
de_genes Output from FindAllMarkers() —
top_genes Top DE genes per group 5
p.cutoff Adjusted p-value threshold 0.05
dot.scale Dot size multiplier 8

See also