CytoProfile (version 0.2.3)

cyt_heatmap: Heat Map.

Description

This function creates a heatmap using the numeric columns from the provided data frame. It supports various scaling options and allows for row or column annotations. The heatmap is saved as a file, with the format determined by the file extension in title.

Usage

cyt_heatmap(
  data,
  scale = c(NULL, "log2", "row_zscore", "col_zscore"),
  annotation_col = NULL,
  annotation_side = c("auto", "row", "col"),
  title = NULL
)

Value

The function does not return a value. It saves the heatmap to a file.

Arguments

data

A data frame containing the input data. Only numeric columns will be used to generate the heatmap.

scale

Character. An optional scaling option. Options are NULL (no scaling), "log2" (log2 transformation), "row_zscore" (z-score scaling by row), or "col_zscore" (z-score scaling by column). Default is NULL.

annotation_col

Character. An optional column name from data to be used for generating annotation colors. Default is NULL.

annotation_side

Character. Specifies whether the annotation should be applied to rows or columns. Options are "auto", "row", or "col".

title

Character. The title of the heatmap and the file name for saving the plot. The file extension (".pdf" or ".png") determines the output format. If NULL, the plot is generated on the current graphics device. Default is NULL.

Author

Shubh Saraswat

Examples

# Load sample data
data("ExampleData1")
data_df <- ExampleData1
# Generate a heatmap with log2 scaling and annotation based on
# the "Group" column
cyt_heatmap(
  data = data_df[, -c(2:3)],
  scale = "log2",  # Optional scaling
  annotation_col = "Group",
  annotation_side = "auto",
  title = NULL
)