plot_simple_heatmap: Plot heatmap

Description

Plot heatmap given a set of markers.

Usage

plot_simple_heatmap(environment, name, markers, path = NA,
  membership = NA, normalized = NA, order = NA, width = 5,
  height = 5, scale = "row", RowSideColors = NA, counts = F,
  filter.diff.exp = F, cellnote = F, key = F, save = NA,
  sort.rows = T, sort.cols = T, Colv = F, Rowv = F,
  dendrogram = "none", main = NA)

Arguments

environment

The environment object

name

The file name of the figure

markers

The markers to be plotted

path

The path where the plot is saved; by default in TMPDIR

membership

The cluster membership

normalized

The normalized data matrix

order

The ordering of markers

width

The width of the pdf figure

height

The height of the pdf figure

scale

character indicating if the values should be centered and scaled in either the row direction or the column direction, or none. The default is "none".

RowSideColors

(optional) character vector of length nrow(x) containing the color names for a vertical side bar that may be used to annotate the rows of x.

counts

Plot count matrix or not

filter.diff.exp

Whether to filter for differentially expressed genes

cellnote

(optional) matrix of character strings which will be placed within each color cell, e.g. p-value symbols.

key

logical indicating whether a color-key should be shown.

save

The path where the plot is saved

sort.rows

Whether to sort rows

sort.cols

Whether to sort columns

Colv

determines if and how the column dendrogram should be reordered. Has the options as the Rowv argument above and additionally when x is a square matrix, Colv="Rowv" means that columns should be treated identically to the rows.

Rowv

determines if and how the row dendrogram should be reordered. By default, it is TRUE, which implies dendrogram is computed and reordered based on row means. If NULL or FALSE, then no dendrogram is computed and no reordering is done. If a dendrogram, then it is used "as-is", ie without any reordering. If a vector of integers, then dendrogram is computed and reordered based on the order of the vector.

dendrogram

character string indicating whether to draw 'none', 'row', 'column' or 'both' dendrograms. Defaults to 'both'. However, if Rowv (or Colv) is FALSE or NULL and dendrogram is 'both', then a warning is issued and Rowv (or Colv) arguments are honoured.

main

main, x- and y-axis titles; defaults to none.