Make a Complex Heatmap From a CellChat Object With Sensible Defaults

This will generate heatmap from a CellChat object using ComplexHeatmap::Heatmap. Options are provided to filter for sender and receiver cells, to generate simple marginal annotations and for aesthetic control.

Usage

bb_cellchat_heatmap(
  object,
  source_filter = NULL,
  target_filter = NULL,
  interaction_filter = NULL,
  interaction_threshold = 0,
  colors = c("transparent", "red3"),
  rowanno = c(NULL, "Annotation", "Pathway"),
  rowanno_colors = NULL,
  colanno = c(NULL, "Source", "Target"),
  colanno_colors = NULL,
  pval_filter = 0.05,
  heatmap_name = "Interaction\nScore",
  heatmap_show_row_dend = TRUE,
  heatmap_row_dend_width = unit(5, "mm"),
  heatmap_show_column_dend = TRUE,
  heatmap_column_dend_height = unit(5, "mm"),
  heatmap_row_names_gp = gpar(fontsize = 10),
  heatmap_column_names_gp = gpar(fontsize = 10),
  heatmap_column_names_rot = 90,
  heatmap_column_title = NULL,
  heatmap_column_title_gp = gpar(fontsize = 12, fontface = "bold"),
  col_anno_name_gp = gpar(fontsize = 10, fontface = "bold"),
  row_anno_name_gp = gpar(fontsize = 10, fontface = "bold"),
  return_value = c("heatmap", "plot", "matrix")
)

Arguments

object

The CellChat object to plot

source_filter

Optional filter for source cell clusters from the object metadata. Accepts a single string or vector of cell groups., Default: NULL

target_filter

Optional filter for target cell clusters from the object metadata. Accepts a single string or vector of cell groups., Default: NULL

interaction_filter

Optional filter to include only certain interactions in the figure.

interaction_threshold

Optional filter to only include interactions above a certain threshold.

colors

Color scale endpoints, Default: c("transparent", "red3")

rowanno

Options for simple row annotation; must be one of c(NULL, "Annotation", "Pathway")

rowanno_colors

Optional colors to replace the poor color selections from Complex heatmap. Must be supplied as a named list with one element each for "Annotation" and "Pathway". Not required if not showing these annotations. The list should be of the form: list(Annotation = c("name1" = "color value1", "name2" = "color_value2")), Default: NULL

colanno

Options for simple column annotation; must be one of c(NULL, "Source", "Target")

colanno_colors

See rowanno_colors, Default: NULL

pval_filter

Filter for significance of associations. CellChat returns pvalues of 0, 0.01, and 0.05; this function will filter and retain values less than or equal to the provided value. Default: 0.05

heatmap_name

Name for the main color scale of the heatmap, Default: 'InteractionScore'

heatmap_show_row_dend

Show row dendrograms? Default: TRUE

heatmap_row_dend_width

Width of row dendrograms Default: unit(5, "mm")

heatmap_show_column_dend

Show column dendrograms?' Default: TRUE

heatmap_column_dend_height

Height of column dendrograms. Default: unit(5, "mm")

heatmap_row_names_gp

Row name graphical params, Default: gpar(fontsize = 10)

heatmap_column_names_gp

Column name graphical params, Default: gpar(fontsize = 10)

heatmap_column_names_rot

Column name rotation, Default: 90

heatmap_column_title

Column title, Default: NULL

heatmap_column_title_gp

Column title graphical params, Default: gpar(fontsize = 12, fontface = "bold")

col_anno_name_gp

Column annotation name graphical params, Default: gpar(fonmtsize = 10, fontface = "bold")

row_anno_name_gp

Row annotation name graphical params, Default: gpar(fontsize = 10, fontface = "bold")

return_value

Return a heatmap plot or a matrix.

Value

a heatmap as a grid object; plot using cowplot::plot_grid

Details

see github::sqjin/CellChat

See also

subsetCommunication as_tibble,c("tibble", "tibble"),rownames filter,mutate,select,mutate-joins,group_by,summarise pivot_wider rowAnnotation,columnAnnotation,draw-dispatch,Heatmap colorRamp2 grid.grab