mgheatmap: Creates a "geneset smart" ComplexHeatmap::Heatmap

Description Usage Arguments Details Value Renaming Heatmap Rows Examples

View source: R/plots-mgheatmap.R

Description

Encapsulates many common "moves" you'll make when trying to make a heatmap, especially if you are trying to show geneset activity across a panel of samples.

NOTE: this function will almost certainly reorder the rows of the input matrix. If you are concatentating Heatmap objects together horizontally (ie. you if you want to use a rowAnnotation along side the returned heatmap), you must reorder the rows of the annotation data.frame, ie. ranno.df <- ranno.df[rownames(out@matrix),]

Usage

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mgheatmap(
  x,
  gdb = NULL,
  col = NULL,
  aggregate.by = c("none", "ewm", "ewz", "zscore"),
  split = TRUE,
  scores = NULL,
  gs.order = NULL,
  name = NULL,
  rm.collection.prefix = TRUE,
  rm.dups = FALSE,
  recenter = FALSE,
  rescale = FALSE,
  center = TRUE,
  scale = TRUE,
  rename.rows = NULL,
  zero_center_colramp = NULL,
  zlim = NULL,
  transpose = FALSE,
  ...
)

Arguments

x

the data matrix

gdb

GeneSetDb object that holds the genesets to plot. Defaults to NULL, which will plot all rows in x.

col

a colorRamp(2) function

aggregate.by

the method used to generate single-sample geneset scores. Default is none which plots heatmap at the gene level

split

introduce row-segmentation based on genesets or collections? Defaults is TRUE which will create split heatmaps based on collection if aggregate.by != 'none', or based on gene sets if aggregate.by == "none".

scores

If aggregate.by != "none" you can pass in a precomupted scoreSingleSamples() result, otherwise one will be computed internally. Note that if this is a data.frame of pre-computed scores, the gdb is largely irrelevant (but still required).

gs.order

This is experimental, and is here to help order the order of the genesets (or genesets collection) in a different way than the default. By default, gs.order = NULL and genesets are enumerated in alphabetical in the heatmap. You can pass in a character vector that will dictate the order of the genesets displayed in the heatmap. Currently this only matches against the "name" value of the geneset and probably only works when split = TRUE. We will support colleciton,name tuples soon. This can be a superset of the names found in gdb. As of ComplexHeatmap v2 (maybe earlier versions), this doesn't really work when cluster_rows = TRUE.

rm.dups

if aggregate.by == 'none', do we remove genes that appear in more than one geneset? Defaults to FALSE

recenter

do you want to mean center the rows of the heatmap matrix prior to calling ComplexHeatmap::Heatmap()?

rescale

do you want to standardize the row variance to one on the values of the heatmap matrix prior to calling ComplexHeatmap::Heatmap()?

rename.rows

defaults to NULL, which induces no action. Specifying a paramter here assumes you want to rename the rows of the heatmap. Please refer to the "Renaming Rows" section for details.

zero_center_colramp

Used to specify the type of color ramp to generate when col is NULL. By default (NULL) we try to guess if we should generate a 0-centered (blue, white, red) color ramp, or an absolute (viridis style) one. The guessing functionality isn't that great, so it doesn't hurt to explicitly set this to TRUE or FALSE.

zlim

Used to control the color saturation of the heatmap when the col parameter is not provided. If NULL, (default), extreme values (outside the c(0.025, 0.975) quantiles) are axed and the colorRamp is based on the remaining value range. If FALSE, the range of the colorRamp is defined by the min/max values. Otherwise a length(2) numeric can be supplied. If the values are between [0,1], then we assume this is a quantile range to be calculated. Otherwise the number are assumed to mark the top and bottom of the color scale range you want to use.

transpose

Flip display so that rows are columns. Default is FALSE.

...

parameters to send down to scoreSingleSamples() or ComplexHeatmap::Heatmap().

Details

More info here.

Value

A Heatmap object.

Renaming Heatmap Rows

This function leverages rename_rows() so that you can better customize the output of your heatmaps by tweaking its rownames.

If you are plotting a gene-level heatmap (ie. aggregate.by == "none"``) and the rownames()are gene identifiers, but you want the rownames of the heatmap to be gene symbols. You can perform this renaming using therename.rows' parameter.

Maybe you are aggregating the expression scores into geneset scores, and you don't want the rownames of the heatmap to be collection;;name (or just name when rm.collection.prefx = TRUE), you can pass in a two column data.frame, where the first column is collection;name and the second is the name you want to rename that to. There is an example of this in the "Examples" section here.

Examples

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library(ComplexHeatmap)
vm <- exampleExpressionSet()
gdb <- exampleGeneSetDb()
col.anno <- ComplexHeatmap::HeatmapAnnotation(
  df = vm$targets[, c("Cancer_Status", "PAM50subtype")],
  col = list(
    Cancer_Status = c(normal = "grey", tumor = "red"),
    PAM50subtype = c(Basal = "purple", Her2 = "green", LumA = "orange")))
mgh <- mgheatmap(vm, gdb, aggregate.by = "ewm", split=TRUE,
                 top_annotation = col.anno, show_column_names = FALSE,
                 column_title = "Gene Set Activity in BRCA subset")

# Maybe you want the rownames of the matrix to use spaces instead of "_"
rr <- geneSets(gdb)[, "name", drop = FALSE]
rr$newname <- gsub("_", " ", rr$name)
mg2 <- mgheatmap(vm, gdb, aggregate.by='ewm', split=TRUE,
                 top_annotation = col.anno, show_column_names = FALSE,
                 column_title = "Gene Set Activity in BRCA subset",
                 rename.rows = rr)

lianos/multiGSEA documentation built on Nov. 17, 2020, 1:26 p.m.