heatmapAlphabet: Draw a customised heatmap where the different variables are...
In barzine/barzinePhdR: Code developed while and for my PhD thesis at the EMBL-EBI

heatmapAlphabet

R Documentation

Draw a customised heatmap where the different variables are sorted alphabetically

Description

Draw a customised heatmap where the different variables are sorted alphabetically

Usage

heatmapAlphabet(data, label.A, label.B, out.A, out.B,
  col = barzinePhdR::colCbc(), digits = 1, key, margins, ...,
  report = TRUE, index = "####", annot = "diag", sorting = TRUE,
  notecol = "grey90", srtCol = 45, cexRow = 1.4, cexCol = 1.4,
  cex.axis = 1.4, mathMethod = "signif", cellAnnot)

Arguments

`data`	correlation (numeric) data.frame to plot
`label.A`	character string. Name of the first data.frame used for the correlation matrix for the additional text.
`label.B`	character string. Name of the second data.frame used for the correlation matrix for the additional text.
`out.A`	character string for the plot (x-axis). Name of the first data.frame used for the correlation matrix
`out.B`	character string for the plot (y-axis). Name of the second data.frame used for the correlation matrix
`col`	color palette to use; default barzinePhdR::colC(), i.e. grDevices::colorRampPalette('aliceblue','darkcyan')
`digits`	default: 1. How many digits should be kept for the annotation.
`key`	boolean. default: TRUE. Whether the key of the heatmap should also be drawn.
`margins`	numeric vector of length 2 containing the margins (see par(mar= *)) for column and row names, respectively.
`...`	other parameters that can be handled by (gplots) heatmap.2
`report`	boolean. Default: TRUE. Output additional text (example for an (r)html report)
`index`	character string. default:"####" Allows to customise the level of indexing through markdown tags.
`annot`	character string. Chose how (if anny annotation) is added to the heatmap 'diag' (default) for the value of the diagonal; 'complete' all the values are added on the heatmap; 'custom' to use the cellAnnot given by user. Anything else returns an heatmap that isn't annotated
`sorting`	boolean; default: TRUE. Whether the input data.frame should be rordered alphabetically before being plotted.
`notecol`	character string specifying the color for cellnote text. Defaults to "grey90".
`srtCol`	angle of column labels, in degrees from horizontal. Default: 45
`cexRow`	positive numbers, used as cex.axis in for the row axis labeling. Default: 1.4
`cexCol`	positive numbers, used as cex.axis in for the column axis labeling. Default: 1.4
`cex.axis`	positive numbers, used as cex.axis in for the row and column axis labeling. Default: 1.4
`mathMethod`	character string that allows to pick how the correlation (in cellnote) should be rounded. Default: "signif"
`cellAnnot`	only if annot=="custom", what to be added on top of the heatmap