Plotting CellPhoneDB results as a heatmap

plot_cpdb_heatmap(
  pvals,
  cell_types = NULL,
  degs_analysis = FALSE,
  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 = TRUE,
  default_sep = "\\|",
  ...
)

Arguments

pvals: Dataframe corresponding to `pvalues.txt` or `relevant_interactions.txt` from CellPhoneDB.
cell_types: vector of cell types to plot. If NULL, all cell types will be plotted.
degs_analysis: Whether `CellPhoneDB` was run in `deg_analysis` mode
log1p_transform: Whether to log1p transform the output.
show_rownames: whether to show row names.
show_colnames: whether to show column names.
scale: scaling mode for pheatmap.
cluster_cols: whether to cluster columns.
cluster_rows: whether to cluster rows.
border_color: border color.
fontsize_row: row font size.
fontsize_col: column font size.
family: font family.
main: plot title.
treeheight_col: height of column dendrogram.
treeheight_row: height of row dendrogram.
low_col: low colour for heatmap.
mid_col: middle colour for heatmap.
high_col: high colour for heatmap.
alpha: pvalue threshold to trim.
return_tables: whether or not to return the results as a table rather than the heatmap
symmetrical: whether or not to return as symmetrical matrix
default_sep: the default separator used when CellPhoneDB was run.
...: passed to pheatmap::pheatmap.

Value

pheatmap object of cellphone db output

Examples

# \donttest{
data(kidneyimmune)
data(cpdb_output2)
plot_cpdb_heatmap(pvals2)

# }