ezheat: Plot heatmap

In jdreyf/ezlimmaplot: Bioinformatics plots using limma and ggplot2, some from output of ezlimma

Plot heatmap

Description

Draw heatmap using pheatmap package.

Usage

ezheat(
  object,
  pheno.df = NULL,
  labrows = rownames(object),
  labcols = colnames(object),
  main = "Log2 Expression",
  name = "topgenes_heat",
  sc = "ctr",
  clip = NA,
  color.v = NULL,
  unique.rows = FALSE,
  only.labrows = FALSE,
  ntop = NULL,
  stat.tab = NULL,
  cutoff = 0.05,
  reorder_rows = FALSE,
  reorder_cols = FALSE,
  gaps_row = NULL,
  gaps_col = NULL,
  annotation_row = NA,
  annotation_colors = NA,
  angle_col = c("270", "0", "45", "90", "315"),
  fontsize_row = 10,
  fontsize_col = 10,
  na.lab = c("---", ""),
  plot = TRUE,
  width = 7,
  height = 7,
  verbose = FALSE
)

Arguments

object	Matrix-like object with features (e.g. genes) as rows and samples as columns.
pheno.df	Data frame with rows as samples and columns as phenotypes.
labrows	Labels for rows, e.g. gene symbols. This can be of length 1 (in which case it is recycled), of length nrow(object).
labcols	Labels for columns. This can be of length 1 (in which case it is recycled), of length ncol(object).
main	Main title of plot.
name	Name of file to create. Set to NA to plot to screen instead of to file.
sc	Row scaling. Should rows be centered ('ctr'), z-scored ('z'), or neither ('none').
clip	Values with magnitude > clip are reset to value clip. If given, must be > 0.
color.v	Color palette for heatmap. If NULL, it's set to colorRampPalette(rev(brewer.pal(n=9, name='RdYlBu')))(50).
unique.rows	Logical; remove duplicated row labels to make rows unique?
only.labrows	Logical; only include rows where labrows aren't missing (missing is defined by na.lab)?
ntop	Scalar number of rows to include.
stat.tab	Matrix-like object with statistics, such as p-values, per column, used to add "*". If given, its dimensions should match object and it cannot have NAs.
cutoff	Cutoff such that elements with stats.tab < cutoff show asterisk if stats.tab and cutoff are not NULL.
reorder_rows	Logical; should rows be reordered with hierarchical clustering?
reorder_cols	Logical; should columns be reordered with hierarchical clustering?
gaps_row	vector of row indices after which to insert gaps.
gaps_col	vector of column indices after which to insert gaps.
annotation_row	data frame that specifies the annotations shown on left side of the heatmap. Each row defines the features for a specific row. The rows in the data and in the annotation are matched using corresponding row names. Note that color schemes takes into account if variable is continuous or discrete.
annotation_colors	list for specifying annotation_row and annotation_col track colors manually. It is possible to define the colors for only some of the features. See pheatmap examples.
angle_col	angle of the column labels, right now one can choose only from few predefined options (0, 45, 90, 270 and 315)
fontsize_row	Font size for row labels.
fontsize_col	Font size for column labels.
na.lab	Character vector of labels in lab.col to treat as missing, in addition to NA.
plot	Logical; should plot be generated?
width	Manual option for determining the output file width in inches.
height	Manual option for determining the output file height in inches.
verbose	Logical; print pruning messages to console?

Details

main is modified to describe data transformations.

If the data after scaling and clipping (if they are used) has positive and negative values, the key is made symmetric about zero.

object cannot have NAs.

Value

A list with element mat of the matrix of values plotted, and if plot=TRUE element gtable, containing the gtable object returned by pheatmap.

jdreyf/ezlimmaplot documentation built on Feb. 8, 2025, 2:25 a.m.