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 = "right",
  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

A character vector or a named list of features to plot. Features can be gene names in Assay or names of numeric columns in meta.data.

assay

Which assay to use. If NULL, the default assay of the Seurat object will be used. When the object also contains ChromatinAssay, the default assay and additional ChromatinAssay will be preprocessed sequentially.

layer

Which layer to use. Default is data.

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

Whether the feature name is labeled in the center of the location of cells with high expression.

label.size

Size of labels.

label.fg

Foreground color of label.

title

The text for the title. Default is NULL.

subtitle

The text for the subtitle for the plot which will be displayed below the title. Default is NULL.

xlab

The x-axis label of the plot. Default is NULL.

ylab

The y-axis label of the plot. Default is NULL.

legend.position

The position of legends, one of "none", "left", "right", "bottom", "top". Default is "right".

theme_use

Theme used. Can be a character string or a theme function. Default is "theme_scop".

theme_args

Other arguments passed to the theme_use. Default is list().

combine

Combine plots into a single patchwork object. If FALSE, return a list of ggplot objects.

ncol

Number of columns in the combined plot. Default is NULL, which means determined automatically based on the number of plots.

return_data

Whether to return plot data along with the plot.

verbose

Whether to print the message. Default is TRUE.

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 <- standard_scop(pancreas_sub, 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")
)
} # }