gene expression data

Description Usage Arguments

This function produces a figure in two panels. On the left is a diamond clustering. On the right is barplot showing the signature size for each element in the clustering.

E3PlotClusteringDiamond(gjh, colmat, gsize, n = 10, spacer = 0.1,
  lab = "All", col.group = NULL, highlight = c(), mai = rep(0.2, 4),
  maxlim = NULL, xticks = seq(0, 300, 100), xticks.dendro = seq(0, 1,
  0.25), lineext = 1.2, multicolor = TRUE, heatcolor = "#282828",
  legend.height = 4, legend.main = "", dendrogram = FALSE,
  dendroheight = 0.8, xlab.right = "Signature size",
  xlab.left = "Jaccard index distance", Rcss = "default",
  Rcssclass = "diamond")

`gjh`	- hclust object. Used to produce diamond clustering on LHS.
`colmat`	- matrix of colors (or values in range [0,1])
`gsize`	- numeric vector with names. Used to produce barplot on RHS.
`n`	- integer. Sets vertical scale. (Set equal or more than number of elements in clustering. Fixing this value helps making multiple clusterings with the same box sizes)
`spacer`	- numeric. Determines empty space between bars on RHS.
`lab`	- character string. Text to write next to clustering on LHS.
`col.group`	- named vector of colors. Associated a color with each element in the clustering.
`highlight`	- character vector. Names of items to highlight on RHS.
`mai`	- numeric vector of length four. Sets margin.
`maxlim`	- numeric. Determines horizontal scale of barplot.
`xticks`	- numeric vector. Values to label on x-axis in the barplot.
`lineext`	- numeric. determines lenght of line labeling highlighted items.
`multicolor`	- logical. Set TRUE to obtain multicolor heatmap. Set FALSE to plot in grayscale
`heatcolor`	- color for heatmap when multicolor is set FALSE.
`legend.height`	- height of legend (in units as number of bars)
`dendrogram`	- logical, set TRUE to replace the heatmap with a dendrogram
`dendroheight`	- numberic, a relative measure for dendrogram width
`xlab.right`	- x-axis label under bar chart
`xlab.left`	- x-axis label under dendrogram
`Rcss`	- Rcss object. Used to style the heatmap with Rcssplot.
`Rcssclass`	- character vector. Classes to tune Rcssplot formatting.