bb_cellchat_heatmap | R Documentation |
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.
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")
)
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. |
see github::sqjin/CellChat
a heatmap as a grid object; plot using cowplot::plot_grid
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
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