Validation result in heatmap format — heatmapTable • GenomicSuperignature

This function subsets validate outputs with different criteria and visualize it in a heatmap-like table.

heatmapTable(
  val_all,
  RAVmodel,
  ind = NULL,
  num.out = 5,
  scoreCutoff = NULL,
  swCutoff = NULL,
  clsizeCutoff = NULL,
  breaks = c(0, 0.5, 1),
  colors = c("white", "white smoke", "red"),
  column_title = NULL,
  row_title = NULL,
  whichPC = NULL,
  filterMessage = TRUE,
  ...
)

Arguments

val_all: An output matrix from validate function with the parameter level = "max". Subset of this matrix is plotted as a heatmap using Heatmap
RAVmodel: PCAGenomicSignatures-class object. RAVmodel used to prepare val_all input.
ind: An integer vector. If this parameter is provided, the other parameters, num.out, scoreCutoff, swCutoff, clsizeCutoff will be ignored and the heatmap table containing only the provided index will be printed.
num.out: A number of highly validated RAVs to output. Default is 5. If any of the cutoff parameters are provided, num.out or the number of filtered RAVs, whichever smaller, will be chosen.
scoreCutoff: A numeric value for the minimum correlation (not include). If val_all input is from multiple studies, the default is 0.7 and this is the only cutoff criteria considered: swCutoff and clsizeCutoff will be ignored.
swCutoff: A numeric value for the minimum average silhouette width.
clsizeCutoff: A integer value for the minimum cluster size.
breaks: A numeric vector of length 3. Number represents the values assigned to three colors. Default is c(0, 0.5, 1).
colors: A character vector of length 3. Each represents the color assigned to three breaks. Default is c("white", "white smoke", "red").
column_title: A character string. Provide the column title.
row_title: A character string. Provide the row title.
whichPC: An integer value between 1 and 8. PC number of your data to check the validated signatures with. Under the default (NULL), it outputs top scored signatures with any PC of your data.
filterMessage: A logical. Under the default TRUE, any output RAV belong to the filtering list will give a message. Silence this message with filterMessage=FALSE. You can check the filter list using data("filterList").
...: any additional argument for Heatmap

Value

A heatmap displaying the subset of the validation result that met the given cutoff criteria. If val_all input is from a single dataset, the output heatmap will contain both score and average silhouette width for each cluster.

If val_all input is from multiple studies, the output heatmap's rows will represent each study and the columns will be RAVs, which meet scoreCutoff for any of the input studies.

Examples

data(miniRAVmodel)
library(bcellViper)
data(bcellViper)

## Single dataset
val_all <- validate(dset, miniRAVmodel)
heatmapTable(val_all, miniRAVmodel, swCutoff = 0)
#> RAV2538 can be filtered based on GSEA_PLIERpriors
#> RAV1139 can be filtered based on GSEA_PLIERpriors
#> RAV884 can be filtered based on GSEA_PLIERpriors
#> RAV438 can be filtered based on GSEA_PLIERpriors
#> RAV725 can be filtered based on GSEA_PLIERpriors


## A list of datasets
val_all2 <- validate(miniTCGA, miniRAVmodel)
heatmapTable(val_all2, miniRAVmodel)