Skip to contents

Heat Map

Source: R/cyt_heatmap.R
cyt_heatmap.Rd

This function creates a heatmap using the numeric columns from the provided data frame. It provides the ability to hide row and column names, adjust font sizes and clustering, and apply additional transformations such as log10 or combined z-scoring. An optional title is displayed as the plot title; an optional filename (ending in .pdf or .png) saves the heat map to disk. Both may be supplied together.

Usage

cyt_heatmap(
  data,
  scale = NULL,
  annotation_col = NULL,
  annotation_side = c("auto", "row", "col"),
  show_row_names = FALSE,
  show_col_names = TRUE,
  fontsize_row = 10,
  fontsize_col = 10,
  font_settings = NULL,
  cluster_rows = TRUE,
  cluster_cols = TRUE,
  title = NULL,
  filename = NULL,
  progress = NULL
)

Arguments

data

A data frame. Only numeric columns are used to construct the heat map.

scale

Character specifying an optional scaling. One of NULL (no scaling), "log2", "log10", "row_zscore", "col_zscore", or "zscore" (apply both row and column z-scoring). Default is NULL.

annotation_col

Optional. Either the name of a column in data or a vector of length equal to the number of rows or columns of the numeric matrix. If a column name is supplied the function determines whether it annotates rows or columns based on its length or the value of annotation_side.

annotation_side

Character. One of "auto" (default), "row", or "col". When "auto" the side is determined by matching the length of annotation_col to rows or columns.

show_row_names

Logical. If TRUE row names are shown. Default is FALSE.

show_col_names

Logical. If FALSE column names are hidden. Default is TRUE.

fontsize_row

Numeric. Font size for row names. Default is 10.

fontsize_col

Numeric. Font size for column names. Default is 10.

font_settings

Optional named list of font sizes for supported heatmap text elements.

cluster_rows

Logical. If TRUE (default), rows are clustered.

cluster_cols

Logical. If TRUE (default), columns are clustered.

title

Character. Optional title displayed at the top of the heat map. If NULL (default), no title is printed.

filename

Character. Optional file path ending in ".pdf" or ".png" (case insensitive). When supplied the heat map is written to disk and screen rendering is suppressed. If NULL (default), the plot is drawn on the active graphics device.

progress

Optional. A Shiny Progress object for reporting progress updates.

Value

Invisibly returns the pheatmap object created by pheatmap::pheatmap().

Author

Shubh Saraswat

Examples

data("ExampleData1")
data_df <- ExampleData1
cyt_heatmap(
  data            = data_df[, -c(2:3)],
  scale           = "log2",
  annotation_col  = "Group",
  annotation_side = "auto",
  title           = "Cytokine Heatmap"
)