Cluster tree plot

Visualize how cells move between clusters across multiple Seurat clustering resolutions.

Usage

ClusterTreePlot(
  srt,
  cluster_cols = NULL,
  prefix = NULL,
  resolutions = NULL,
  features = NULL,
  assay = NULL,
  layer = "data",
  edge_threshold = 0,
  node_palette = "Spectral",
  node_palcolor = NULL,
  edge_palette = "YlOrRd",
  edge_palcolor = NULL,
  node_size = c(3, 10),
  edge_size = c(0.25, 1.8),
  label = TRUE,
  label.size = 3,
  label.fg = "black",
  title = "Cluster tree",
  subtitle = NULL,
  xlab = "Resolution",
  ylab = "Cluster",
  legend.position = "bottom",
  theme_use = "theme_scop",
  theme_args = list(),
  combine = TRUE,
  ncol = NULL,
  return_data = FALSE,
  verbose = TRUE
)

Arguments

srt

A Seurat object.

cluster_cols

Metadata columns containing clustering results at different resolutions. If NULL, columns generated by Seurat::FindClusters(resolution = c(...)) are detected automatically.

prefix

Optional prefix used to filter automatically detected clustering columns, for example "RNA_snn".

resolutions

Optional numeric vector used to filter automatically detected resolutions.

features

Features to plot: a character vector or a named list of assay gene names or numeric metadata columns.

assay

Assay to use. NULL uses the default assay.

layer

Assay layer to use.

edge_threshold

Minimum incoming proportion required to draw an edge. Edges below this threshold are still available when return_data = TRUE.

node_palette, node_palcolor

Palette used for node colors.

edge_palette, edge_palcolor

Palette used for edge colors.

node_size

Numeric range used for node sizes.

edge_size

Numeric range used for edge widths.

label

Label high-expressing cells.

label.size

Group labels. label_insitu = FALSE uses numbers instead of group names.

label.fg

Group labels. label_insitu = FALSE uses numbers instead of group names.

title

Plot title. NULL hides the title for merged/single panels. When multiple lineages are plotted and title is NULL, each panel is titled with its lineage column.

subtitle

Plot subtitle.

xlab

Plot labels.

ylab

Plot labels.

legend.position

The position of the legend. The default is "bottom" to keep the multiple cluster-tree guides compact.

theme_args

Theme name or function, plus extra theme arguments.

combine

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

ncol

Number of columns of the combined plot.

return_data

Whether to return plot data along with the plot.

verbose

Whether to print messages.

Value

A ggplot, patchwork, list of ggplot objects, or a list with plot data when return_data = TRUE.

Examples

if (FALSE) { # \dontrun{
data(pancreas_sub)
pancreas_sub <- RunStandardWorkflow(pancreas_sub, verbose = FALSE)
pancreas_sub <- Seurat::FindNeighbors(
  pancreas_sub,
  dims = 1:20,
  verbose = FALSE
)
pancreas_sub <- Seurat::FindClusters(
  pancreas_sub,
  resolution = seq(0.2, 1, by = 0.2),
  verbose = FALSE
)
ClusterTreePlot(pancreas_sub)

ClusterTreePlot(
  pancreas_sub,
  features = c("Ins1", "Gcg")
)
} # }