SCENICPlot() with tool_name = "SCENICPlus" and assay = "scenicplus".
Default "heatmap_dotplot": color = TF expression, size = RSS.
Usage
SCENICPlusPlot(
object,
group.by,
tool_name = "SCENICPlus",
assay = "scenicplus",
plot_type = c("heatmap_dotplot", "rss_rank", "rss_heatmap", "rss_dotplot",
"eregulon_dim", "activity_cor_dumbbell", "regulon_size", "network_graph", "network",
"egrn", "overlap", "target_bar", "coverage"),
srt = NULL,
...
)Arguments
- object
A Seurat object from
RunSCENICPlus().- group.by
Metadata column for cell groups.
- tool_name
Tools slot. Default
"SCENICPlus".- assay
ERegulon AUC assay. Default
"scenicplus".- plot_type
Plot type. Default
"heatmap_dotplot".- srt
Deprecated alias for
object; supply exactly one of the two. It will be removed in scop 1.0.0.- ...
Arguments passed to other functions.
Value
Same as SCENICPlot().
Examples
if (FALSE) { # \dontrun{
data(pancreas_sub)
pancreas_sub <- RunStandardWorkflow(pancreas_sub)
pancreas_sub <- RunSCENICPlus(
pancreas_sub,
backend = "python",
python_result_dir = "test/scenicplus"
)
scenicplus_dot <- SCENICPlusPlot(pancreas_sub, group.by = "CellType")
example_tfs <- unique(scenicplus_dot$top_table$TF)[1:3]
regulons <- head(rownames(pancreas_sub[["scenicplus"]]), 6)
GroupHeatmap(
pancreas_sub, group.by = "CellType", features = regulons,
assay = "scenicplus", layer = "data", exp_method = "raw",
lib_normalize = FALSE
)$plot
FeatureStatPlot(
pancreas_sub, group.by = "CellType", stat.by = regulons,
assay = "scenicplus", layer = "data", plot_type = "violin"
)
FeatureDimPlot(
pancreas_sub, features = regulons, assay = "scenicplus",
layer = "data", reduction = "UMAP"
)
SCENICPlusPlot(pancreas_sub, group.by = "CellType", plot_type = "egrn", features = example_tfs)
SCENICPlusPlot(
pancreas_sub,
group.by = "CellType", plot_type = "network_graph", features = example_tfs
)
} # }