mHeatmapTC: Wrapper around heatmap.2; allows to annotate with the colours...
In barzine/barzinePhdR: Code developed while and for my PhD thesis at the EMBL-EBI

mHeatmapTC

R Documentation

Wrapper around heatmap.2; allows to annotate with the colours on the side. Colours are the transpose of mHeatmap

Description

Wrapper around heatmap.2; allows to annotate with the colours on the side. Colours are the transpose of mHeatmap

Usage

mHeatmapTC(DF, method = "pearson", use = "pairwise.complete.obs",
  hclustMethod = "ward.D", trace = "none", dendrogram = "row", col,
  cexRow = 1, cexCol = 1, annotate = FALSE, signifdigit = 1,
  rowsidecolors, colsidecolors, notecol = "black",
  ColsideMode = "match", RowsideMode = "extract", srtCol = 45,
  margins = c(12, 8), common.cond, datasetCol, TissueCol, baseFont, ...,
  parenthesis = TRUE, key.title)

Arguments

`DF`	data.frame or matrix to use for the heatmap
`method`	string to pick the method with which to compute the correlation. One of "pearson" (default), "kendall", or "spearman"
`use`	character string giving a method for computing covariances in the presence of missing values. This must be (an abbreviation of) one of the strings "everything" (default), "all.obs", "complete.obs", "na.or.complete", or "pairwise.complete.obs".
`hclustMethod`	character string. he agglomeration method to be used. This should be (an unambiguous abbreviation of) one of "ward.D", "ward.D2", "single", "complete", "average" (= UPGMA), "mcquitty" (= WPGMA), "median" (= WPGMC) or "centroid" (= UPGMC).
`trace`	character string indicating whether a solid "trace" line should be drawn across 'row's or down 'column's, 'both' or 'none'. The distance of the line from the center of each color-cell is proportional to the size of the measurement. Defaults to 'none'.
`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.
`col`	colors used for the image. Defaults to col=colorRampPalette(c('ghostwhite','darkcyan'))
`cexRow`, `cexCol`	positive numbers, used as cex.axis in for the row or column axis labeling. The defaults currently only use number of rows or columns, respectively.
`annotate`	boolean. Whether to add the correlations as annotation on the heatmap
`signifdigit`	integer. Number of digit to show for the correlation showed as annotation. Default:1
`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. Otherwise can be created internally
`colsidecolors`	(optional) character vector of length ncol(x) containing the color names for a horizontal side bar that may be used to annotate the columns of x. Otherwise can be created internally
`notecol`	character string. Colour for the annotation
`ColsideMode`	character string that allows to create the annotation colours based on the column names one of the following strings: 'extract', 'extractSpace', 'extract2' or 'extractSpace2'
`RowsideMode`	character string that allows to create the annotation colours based on the row names (of the correlation matrix) one of the following strings: 'match', 'extract' or 'extractSpace'
`srtCol`	angle of column labels, in degrees from horizontal. Default: 45
`margins`	numeric vector of length 2 containing the margins (see par(mar= *)) for column and row names, respectively. Default: c(8,12)
`common.cond`	argument for matchColCond
`datasetCol`	colour palette for the datasets in the form of a named vector
`TissueCol`	colour palette for the tissues in the form of a named vector
`baseFont`	character string. Allows to pick the font of the figure
`...`	other parameters that can be used by heatmap.2
`parenthesis`	boolean. Whether the column names comprises parenthesis
`key.title`	main title of the color key. If set to NA no title will be plotted.