Generate Heatmap for Signature Data — sig

Creates a heatmap from signature data with grouping variables, offering flexible options for colors, clustering, and output formats using ComplexHeatmap.

Usage

sig_pheatmap(
  input,
  feas,
  group,
  group2 = NULL,
  group3 = NULL,
  ID = "ID",
  path = NULL,
  cols1 = "random",
  cols2 = "random",
  cols3 = "random",
  seed = 54321,
  show_col = FALSE,
  palette1 = 1,
  palette2 = 2,
  palette3 = 3,
  cluster_cols = TRUE,
  palette_for_heatmape = 6,
  scale.matrix = TRUE,
  cellwidth = 1,
  cellheight = 9,
  show_colnames = FALSE,
  fig.type = "pdf",
  width = 6,
  height = NULL,
  file_name_prefix = 1
)

Arguments

input: Data frame with variables in columns.
feas: Character vector. Feature names (columns) to include in heatmap.
group: Character string. Column name for primary grouping variable.
group2: Character string or `NULL`. Optional secondary grouping variable.
group3: Character string or `NULL`. Optional tertiary grouping variable.
ID: Character string. Column name for sample identifiers. Default is `"ID"`.
path: Character string or `NULL`. Directory to save output files. Default creates `"Marker-heatmap-average"`.
cols1: Character vector or `"random"` or `"normal"`. Colors for primary group. Default is `"random"`.
cols2: Character vector or `"random"` or `"normal"`. Colors for secondary group. Default is `"random"`.
cols3: Character vector or `"random"` or `"normal"`. Colors for tertiary group. Default is `"random"`.
seed: Integer. Random seed for color generation. Default is `54321`.
show_col: Logical indicating whether to display colors. Default is `FALSE`.
palette1: Integer. Palette for primary group. Default is `1`.
palette2: Integer. Palette for secondary group. Default is `2`.
palette3: Integer. Palette for tertiary group. Default is `3`.
cluster_cols: Logical indicating whether to cluster columns. Default is `TRUE`.
palette_for_heatmape: Integer. Palette number for heatmap. Default is `6`.
scale.matrix: Logical indicating whether to scale the matrix. Default is `TRUE`.
cellwidth: Numeric. Width of each cell in points. Default is `1`.
cellheight: Numeric. Height of each cell in points. Default is `9`.
show_colnames: Logical indicating whether to show column names. Default is `FALSE`.
fig.type: Character string. File format for saving. Default is `"pdf"`.
width: Numeric. Width of saved figure in inches. Default is `6`.
height: Numeric or `NULL`. Height of saved figure in inches. Calculated if `NULL`.
file_name_prefix: Character or numeric. Prefix for saved file name. Default is `1`.

Value

A list containing:

p_anno: Annotation data frame
p_cols: List of cluster colors
plot: ComplexHeatmap object
eset: Transformed expression matrix

Author

Dongqiang Zeng

Examples

tcga_stad_sig <- load_data("tcga_stad_sig")
tcga_stad_pdata <- load_data("tcga_stad_pdata")
input <- merge(tcga_stad_pdata, tcga_stad_sig, by = "ID")
feas <- grep("MCPcounter", colnames(input), value = TRUE)
sig_pheatmap(
  input = input, feas = feas, group = "subtype",
  scale.matrix = TRUE, path = tempdir()
)
#> ℹ Heatmap palettes: 1 (pheatmap), 2 (peach), 3 (blues), 4 (virids), 5 (reds), 6 (RdBu), 7 (navy_firebrick), 8 (magma)
#> ℹ Random palettes: 1 (palette1), 2 (palette2), 3 (palette3), 4 (palette4)
#> ℹ Using random seed: 54321
#> $subtype
#>         EBV          GS         CIN         MSI 
#> "#8F7700FF"   "#386CB0" "#008B45FF"   "#e31a1c" 
#> 
#> ✔ Heatmap saved to: /tmp/RtmpMGdUJv/1-pheatmap-subtype.pdf