Plot SCENIC or SCENIC+ regulon activity

Plot RSS and regulon activity from RunSCENIC() or RunSCENICPlus(). Use SCENICPlusPlot() for SCENIC+ defaults. Network palette = "RdYlBu" uses "Chinese". "network" draws one hub per TF. Network plots have no title. When one TF has multiple regulons, network legends show the regulon with the highest RSS; the corresponding cell type and score remain available in the returned annotation table.

Usage

SCENICPlot(
  srt,
  group.by,
  tool_name = "SCENIC",
  assay = "scenic",
  layer = "data",
  plot_type = c("rss_rank", "rss_heatmap", "rss_dotplot", "heatmap_dotplot",
    "activity_heatmap", "activity_violin", "activity_dim", "eregulon_dim",
    "activity_cor_dumbbell", "regulon_size", "network_graph", "network", "egrn",
    "overlap", "target_bar", "coverage"),
  features = NULL,
  reduction = NULL,
  dims = c(1, 2),
  cor.features = NULL,
  cor.feature.labels = NULL,
  cor_method = c("spearman", "pearson", "kendall"),
  p_cutoff = 0.05,
  cor_sort.by = c("difference", "max_abs", "input"),
  cor_cols = c("#56B4E9", "#E83F6F"),
  cor_xlim = NULL,
  cor_label = TRUE,
  top_n = 12,
  regulon_label = c("auto", "regulon", "tf"),
  rss_rank_yscale = c("shared", "free"),
  activity_scale = FALSE,
  rss_scale = FALSE,
  heatmap_show_row_names = FALSE,
  heatmap_show_column_names = FALSE,
  heatmap_cluster_rows = TRUE,
  heatmap_cluster_columns = FALSE,
  heatmap_order = c("cluster", "group", "input"),
  heatmap_row_names_side = "right",
  heatmap_column_names_side = "top",
  heatmap_row_names_rot = 0,
  heatmap_column_names_rot = 45,
  heatmap_border = TRUE,
  heatmap_palette = NULL,
  heatmap_palcolor = NULL,
  heatmap_group_palette = "Chinese",
  heatmap_group_palcolor = NULL,
  heatmap_limits = NULL,
  heatmap_args = list(),
  palette = "RdYlBu",
  palcolor = NULL,
  compare_expression = FALSE,
  expression_assay = NULL,
  expression_layer = "data",
  expression_scale = TRUE,
  dim_args = list(),
  atac_assay = NULL,
  extend.upstream = 50000,
  extend.downstream = 50000,
  coverage_args = list(),
  max_targets = 20,
  max_edges = Inf,
  network_layout = c("auto", "star", "hub", "tripartite", "kk", "fr"),
  network_tf = NULL,
  network_include_regions = TRUE,
  label_nodes = c("auto", "tfs", "all", "none"),
  network_label_top_n = 60,
  combine = TRUE,
  ncol = 3,
  return_data = TRUE,
  title = NULL,
  point_color = "#B8C2CC",
  top_color = "#B64342",
  point_size = 1.8,
  point_alpha = 0.85,
  highlight_tf = NULL,
  highlight_color = "#7A0177",
  highlight_point_size = 2,
  highlight_linewidth = 0.5,
  label_size = 3,
  label_max_overlaps = Inf,
  verbose = TRUE,
  ...
)

Arguments

srt

A Seurat object with SCENIC or SCENIC+ results.

group.by

Metadata column for cell groups.

tool_name

srt@tools entry. Default "SCENIC".

assay

Fallback assay for regulon activity.

layer

Assay layer for regulon activity.

plot_type

One of "rss_rank", "rss_heatmap", "rss_dotplot", "heatmap_dotplot", "activity_heatmap", "activity_violin", "activity_dim", "eregulon_dim", "activity_cor_dumbbell", "regulon_size", "network", "network_graph", "egrn", "overlap", "target_bar", "coverage".

features

TF or regulon names.

reduction

Reduction for "activity_dim" / "eregulon_dim".

dims

Two reduction dimensions.

cor.features

Two metadata columns or genes for "activity_cor_dumbbell".

cor.feature.labels

Optional legend labels for cor.features.

cor_method

Correlation method for "activity_cor_dumbbell".

p_cutoff

Significance cutoff for "activity_cor_dumbbell".

cor_sort.by

Row order: "difference", "max_abs", or "input".

cor_cols

Two colors for the two correlation targets.

cor_xlim

Optional x-axis limits for the dumbbell plot.

cor_label

Whether to label dumbbell points.

top_n

Top regulons per group.

regulon_label

Label source for RSS rank plots and network legends. "auto" keeps TF-only labels when a TF has one regulon and shows the regulon name when multiple regulons share a TF; "regulon" always shows regulon names; "tf" always shows TF names.

rss_rank_yscale

Use a "shared" y-axis across RSS rank panels for direct score comparison, or "free" for the legacy per-panel scale.

activity_scale

Z-score regulons in "activity_heatmap".

rss_scale

Z-score regulons in "rss_heatmap".

heatmap_show_row_names, heatmap_show_column_names

Heatmap names.

heatmap_cluster_rows, heatmap_cluster_columns

Heatmap clustering.

heatmap_order

"cluster", "group", or "input".

heatmap_row_names_side, heatmap_column_names_side

Name sides.

heatmap_row_names_rot, heatmap_column_names_rot

Name rotation.

heatmap_border

Heatmap borders.

heatmap_palette, heatmap_palcolor

Heatmap palette.

heatmap_group_palette, heatmap_group_palcolor

Group annotation palette.

heatmap_limits

Color-scale limits for RSS/activity heatmaps.

heatmap_args

Extra arguments for GroupHeatmap() / FeatureHeatmap().

palette, palcolor

Palette for RSS, size, target, and network colors.

compare_expression

Add TF expression next to "activity_dim".

expression_assay, expression_layer

Assay and layer for TF expression.

expression_scale

Z-score TF expression in "heatmap_dotplot".

dim_args

Extra arguments for FeatureDimPlot() / CellDimPlot().

atac_assay

Chromatin assay for "coverage".

extend.upstream, extend.downstream

Flanks for "coverage".

coverage_args

Extra arguments for CoverageTrackPlot().

max_targets

Max targets per TF in network plots.

max_edges

Max edges in "network_graph".

network_layout

"auto", "star", "kk", "hub", "tripartite", "fr". "network" uses "star" for one TF and "hub" for several.

network_tf

TFs for "network" / "egrn".

network_include_regions

Use SCENIC+ triplets when stored.

label_nodes

"auto", "tfs", "all", or "none".

network_label_top_n

Max TF labels in "network_graph".

combine

Combine plots with patchwork. combine = FALSE returns a list of ggplots.

ncol

Number of columns of the combined plot.

return_data

Return RSS tables with plots.

title

Optional combined-plot title. Ignored by "network", "network_graph", and "egrn".

point_color

Rank-plot point color.

top_color

Top-regulon point color.

point_size

Point size.

point_alpha

Rank-plot alpha.

highlight_tf

TFs or regulons to highlight.

highlight_color

Highlight color.

highlight_point_size

Highlight point size.

highlight_linewidth

Highlight line width.

label_size

Top-regulon label size.

label_max_overlaps

Max overlapping labels.

verbose

Print messages.

...

Extra heatmap arguments such as width and height.

Value

Plot, or a list with rss_matrix, rank_table, top_table, plots, and plot when return_data = TRUE.

See also

RunSCENIC, RunSCENICPlus, SCENICPlusPlot

Examples

if (FALSE) { # \dontrun{
data(pancreas_sub)
pancreas_sub <- RunStandardWorkflow(pancreas_sub)
pancreas_sub <- RunSCENIC(
  pancreas_sub,
  species = "Mus_musculus",
  backend = "cpp",
  work_dir = "test/scenic"
)
scenic_rss <- SCENICPlot(pancreas_sub, group.by = "CellType", plot_type = "rss_rank")
example_tfs <- unique(scenic_rss$top_table$TF)[1:3]
SCENICPlot(pancreas_sub, group.by = "CellType", plot_type = "heatmap_dotplot")
SCENICPlot(pancreas_sub, group.by = "CellType", plot_type = "network", features = example_tfs)
SCENICPlot(pancreas_sub, group.by = "CellType", plot_type = "network_graph", features = example_tfs)
SCENICPlusPlot(pancreas_sub, group.by = "CellType", plot_type = "egrn", features = example_tfs)
SCENICPlusPlot(pancreas_sub, group.by = "CellType", plot_type = "coverage", features = example_tfs)
} # }