rsScoreHeatmap: Heatmap of region set scores

In databio/COCOA: Coordinate Covariation Analysis

Heatmap of region set scores

Description

Heatmap of the ranking of region set scores across target variables. A visualization of the rank of region sets in each target variable, allowing the user to see if a region set is ranked highly for all target variables or only a subset. Region sets will be ranked from highest scoring to lowest based on their score for 'orderByCol'. The ComplexHeatmap package is used and additional parameters for the ComplexHeatmap::Heatmap function may be passed to this function to modify the heatmap.

Usage

rsScoreHeatmap(
  rsScores,
  signalCol = paste0("PC", 1:5),
  orderByCol = "PC1",
  rsNameCol = "rsName",
  topX = 20,
  col = c("red", "#EEEEEE", "blue"),
  row_title = "Region Set",
  column_title = "Principal Component",
  column_title_side = "bottom",
  cluster_rows = FALSE,
  cluster_columns = FALSE,
  show_row_names = TRUE,
  row_names_max_width = unit(10000, "mm"),
  name = "Rank within PC",
  ...
)

Arguments

rsScores	data.frame. A data.frame with region set scores. The output of the 'aggregateSignalGRList' function. Each row is a region set. One column for each sample variable of interest (e.g. PC or sample phenotype). Also can have columns with info on the overlap between the region set and the epigenetic data. Rows should be in the same order as the region sets in GRList (the list of region sets used to create rsScores.)
signalCol	A character vector with the names of the sample variables of interest/target variables (e.g. PCs or sample phenotypes). Must be column names of rsScores.
orderByCol	A character object. Target variable to order by in heatmap (arranged in decreasing order for scores so p values should be -log transformed). Must be the name of a column in rsScores.
rsNameCol	Character. Name of the column in rsScores that has the names/identifiers for the region sets so these can be included in the plot as row names.
topX	Number of top region sets to include in the heatmap
col	A vector of colors or a color mapping function which will be passed to the ComplexHeatmap::Heatmap() function. See ?Heatmap (the "col" parameter) for more details. "#EEEEEE" is the code for a color similar to white.
row_title	Character object, row title
column_title	Character object, column title
column_title_side	Character object, where to put the column title: "top" or "bottom"
cluster_rows	Logical object, whether rows should be clustered. This should be kept as FALSE to keep the correct ranking of region sets.
cluster_columns	Logical object, whether to cluster columns. It is recommended to keep this as FALSE so it will be easier to compare target variables that are ordered (such as principal components). With cluster_columns = FALSE, they will be in the same specified order in different heatmaps.
show_row_names	Logical object, display row names (ie region set names)
row_names_max_width	"unit" object. The amount of room to allocate for row names. See ?grid::unit for object type.
name	Character object, legend title
...	Optional parameters for ComplexHeatmap::Heatmap().

Value

A heatmap of region set scores across. Each row is a region set, each column is a target variable. The color corresponds to the relative rank of a region set's score for a given target variable out of all tested region sets.

Examples

data("rsScores")
scoreHeatmap <- rsScoreHeatmap(rsScores, 
          signalCol=paste0("PC", 1:2), orderByCol = "PC2")

databio/COCOA documentation built on Sept. 1, 2023, 5:50 p.m.