SpaCCI (version 1.0.4)

plot_SpaCCI_heatmap: Plot SpaCCI Results on the heatmap Visualize inferred significant cell-cell interactions using a heatmap

Description

Plot SpaCCI Results on the heatmap Visualize inferred significant cell-cell interactions using a heatmap

Usage

plot_SpaCCI_heatmap(
  SpaCCI_Result_List,
  specific_celltypes = NULL,
  pathways = NULL,
  interaction = NULL,
  log1p_transform = FALSE,
  show_rownames = TRUE,
  show_colnames = TRUE,
  scale = "none",
  cluster_cols = TRUE,
  cluster_rows = TRUE,
  border_color = "white",
  fontsize_row = 11,
  fontsize_col = 11,
  family = "Arial",
  main = "",
  treeheight_col = 0,
  treeheight_row = 0,
  low_col = "dodgerblue4",
  mid_col = "peachpuff",
  high_col = "deeppink4",
  alpha = 0.05,
  return_tables = FALSE,
  symmetrical = FALSE,
  ...
)

Value

If `return_tables` is FALSE (default), the function returns a heatmap object created by pheatmap, showing the count of significant cell-cell interactions. If `return_tables` is TRUE, the function returns a list containing:

heatmap

The heatmap object showing the significant cell-cell interactions.

heatmap_countmatrix

The matrix used to generate the heatmap, with cell types as rows and columns, and counts of significant interactions as values.

table

A data frame summarizing the counts of significant interactions between each ligand and receptor cell type combination.

Arguments

SpaCCI_Result_List

A list containing the results from a SpaCCI "regional" or "global" analysis. This list should include pvalue_df, which are the outputs from run_SpaCCI(..., analysis_scale = "regional",...) or run_SpaCCI(..., analysis_scale = "global",...).

specific_celltypes

A vector of cell types to include in the heatmap, i.e c("Celltype_A","Celltype_B"). NOTE: the cell type names should match the names input in the SpaCCI analysis.

pathways

A vector of pathways to filter the interactions. Initially set to NULL, if not, then it will aggregate the results of the selected pathways.

interaction

A vector of interactions to filter. Initially set to NULL, if not, then it will aggregate the results of the selected interactions.

log1p_transform

Logical; whether to apply a log(1 + x) transformation to the count matrix.

show_rownames

Logical; whether to show row names in the heatmap.

show_colnames

Logical; whether to show column names in the heatmap.

scale

Character; whether to scale the data ("row", "column", "none").

cluster_cols

Logical; whether to cluster columns.

cluster_rows

Logical; whether to cluster rows.

border_color

Character; color of the heatmap borders.

fontsize_row

Numeric; font size for row names.

fontsize_col

Numeric; font size for column names.

family

Character; font family for text in the heatmap.

main

Character; title of the heatmap.

treeheight_col

Numeric; height of the column dendrogram.

treeheight_row

Numeric; height of the row dendrogram.

low_col

Character; color for low values in the heatmap.

mid_col

Character; color for mid values in the heatmap.

high_col

Character; color for high values in the heatmap.

alpha

Numeric; significance threshold for p-values, initailly set to 0.05.

return_tables

Logical; whether to return the count matrix and summary tables.

symmetrical

Logical; whether to make the heatmap symmetrical.

...

Additional arguments passed to `pheatmap`.

Examples

library(SpaCCI)
library(dplyr)
library(reshape2)
library(grDevices)
library(pheatmap)
data(result_global)
celltypes <- c("beta" , "delta" , "ductal","macrophage",
                "activated_stellate", "quiescent_stellate")
plot_SpaCCI_heatmap(SpaCCI_Result_List = result_global,
                    symmetrical = FALSE, cluster_cols = FALSE, return_tables = FALSE,
                    cluster_rows = FALSE, #cellheight = 10, cellwidth = 10,
                    specific_celltypes = c(celltypes),
                    main= "Cell-Cell Interaction Count")