visqc_heatmap: easier heatmaps

In rmflight/visualizationQualityControl: Development of visualization methods for quality control

easier heatmaps

Description

rolls some of the common Heatmap options into a single function call to make life easier when creating lots of heatmaps. Note: clustering of rows and columns is disabled, it is expected that you are reordering the matrix beforehand, or passing in column_order and row_order as arguments to be passed to Heatmap (see example). Matrices can be reordered using similarity_reorderbyclass, and nice class colors generated using generate_group_colors

Usage

visqc_heatmap(
  matrix_data,
  color_values,
  title = "",
  row_color_data = NULL,
  row_color_list = NULL,
  col_color_data = NULL,
  col_color_list = NULL,
  ...
)

Arguments

matrix_data	the matrix you want to plot as a heatmap
color_values	the color mapping of values to colors (see Details)
title	what do the values represent
row_color_data	data for row annotations
row_color_list	list for row annotations
col_color_data	data for column annotations
col_color_list	list for column annotations
...	other Heatmap parameters

Details

This function uses the ComplexHeatmap package to produce heatmaps with complex row- and column-color annotations. Both row_color_data and col_color_data should be data.frame's where each column describes meta-data about the rows or columns of the matrix. The row_color_list and col_color_list provide the mapping of color to annotation, where each list entry should be a named vector of colors, with the list entry corresponding to a column entry in the data.frame, and the names of the colors corresponding to annotations in that column.

Examples

 
## Not run: 
library(circlize)
data(grp_cor)
data(grp_info)
colormap <- colorRamp2(c(0, 1), c("black", "white"))

annotation_color <- c(grp1 = "green", grp2 = "red", set1 = "blue",
                      set2 = "yellow")

row_data <- grp_info[, "grp", drop = FALSE]
col_data <- grp_info[, "set", drop = FALSE]
row_annotation = list(grp = annotation_color[1:2])
col_annotation = list(set = annotation_color[3:4])

visqc_heatmap(grp_cor, colormap, row_color_data = row_data, row_color_list = row_annotation,
                 col_color_data = col_data, col_color_list = col_annotation)
                 
reorder_sim <- similarity_reorderbyclass(grp_cor, transform = "sub_1")
visqc_heatmap(grp_cor, colormap, "reorder1", row_data, row_annotation, col_data, col_annotation,
                 column_order = reorder_sim$indices, row_order = reorder_sim$indices)

sample_classes <- grp_info[, "grp", drop = FALSE]
reorder_sim2 <- similarity_reorderbyclass(grp_cor, sample_classes, "sub_1")
visqc_heatmap(grp_cor, colormap, "reorder2", row_data, row_annotation, col_data, col_annotation,
                 column_order = reorder_sim2$indices, row_order = reorder_sim2$indices)

## End(Not run)

rmflight/visualizationQualityControl documentation built on Feb. 18, 2024, 9:46 a.m.