do_TFActivityHeatmap() | Transcription factor activity

TF activity heatmaps visualize DoRothEA transcription factor activity scores from decoupleR. Shows which transcription factors are most active in different cell populations.

Due to dependency problems with OmnipathR, this page will not show plots as it can not compute.

Basic usage

First compute TF activities using decoupleR:

# Run decoupleR with DoRothEA prior knowledge
net <- decoupleR::get_dorothea(organism = "human", levels = c("A", "B", "C"))
activities <- decoupleR::run_wmean(mat = as.matrix(sample[["RNA"]]$data), 
                                   net = net)

p <- SCpubr::do_TFActivityHeatmap(sample = sample,
                                  activities = activities)
p

Limit number of TFs

p <- SCpubr::do_TFActivityHeatmap(sample = sample,
                                  activities = activities,
                                  n_tfs = 10)
p

Select specific TFs

p <- SCpubr::do_TFActivityHeatmap(sample = sample,
                                  activities = activities,
                                  tfs.use = c("PAX5", "STAT3", "NF-kB"))
p

Group by custom variable

p <- SCpubr::do_TFActivityHeatmap(sample = sample,
                                  activities = activities,
                                  group.by = "cell_type")
p

Split by condition

p <- SCpubr::do_TFActivityHeatmap(sample = sample,
                                  activities = activities,
                                  split.by = "condition")
p

Show values

p <- SCpubr::do_TFActivityHeatmap(sample = sample,
                                  activities = activities,
                                  values.show = TRUE,
                                  values.size = 4)
p

Parameter reference

Note

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

Core parameters

Parameter Description Default
activities DecoupleR output with DoRothEA —
n_tfs Number of top TFs 25
tfs.use Specific TFs to include NULL
statistic Activity statistic "norm_wmean"
return_object Return data along with plot FALSE

Values display

Parameter Description Default
values.show Show numeric values FALSE
values.size Value text size 3
values.threshold Threshold on which the text changes color NULL
values.round Decimal places 1

See also