HeatMap: Heat map
In NormalizeMets: Analysis of Metabolomics Data

Description Usage Arguments Author(s) See Also Examples

Produces an interactive or a non-interactive heat map of a metabolomics data matrix optionally clustered according to specified methods

HeatMap(featuredata, groupdata, saveplot = FALSE, plotname = "heatmap",
  savetype = c("png", "bmp", "jpeg", "tiff", "pdf"), interactiveplot = TRUE,
  saveinteractiveplot = FALSE, return.interactive = FALSE,
  numeric.mets = FALSE, colramp = c(75, "magenta", "green"),
  scale = c("row", "column", "none"), dendrogram = c("column", "row",
  "both", "none"), distmethod = "euclidean", aggmethod = "complete",
  margins = c(5, 5), key = TRUE, keysize = 1.5, cexRow = 0.5,
  ColSideColors = NULL, ...)

`featuredata`	A data frame in the met data format. This should have sample names in the first column to be read as row names and the metabolomics variables in the remaining columns.
`groupdata`	A data frame or a table with optional sample names in the first column to be read as row names and group names in the following column.
`saveplot`	A logical indication whether to save the plot produced.
`plotname`	Name of the output file if the file is to be saved.
`savetype`	The required format for the plot to be saved in. Threre is a choice of `"png","bmp","jpeg","tiff","pdf"` type files.
`interactiveplot`	A logical indication whether an interactive plot is to be shown.
`saveinteractiveplot`	A logical indication whether to save the interactive plot as an `"html"` file.
`return.interactive`	A logical indication whether an interactive plot should be returned as a variable by the function.
`numeric.mets`	A logical indication whether metabolite names are numeric. If `TRUE`, "m" is added before each metabolite name displyed on the graph.
`colramp`	A vector containing (in order), the desired number of color elements in the panel, color to use for the lowest, color to use for the highest for the non-interactive plot.
`scale`	A character indicating if the values should be scaled metabolite-wise ("`row`") or group-wise ("`column`").
`dendrogram`	A character indicating whether to draw "`none`", "`row`", "`column`" or "`both`" dendrograms for non-interactive plots.
`distmethod`	The distance measure to be used. This must be one of "`euclidean`", "`maximum`", "`manhattan`", "`canberra`", "`binary`" or "`minkowski`".
`aggmethod`	The agglomeration method to be used. This should be one of "`ward`", "`single`", "`complete`", "`average`", "`mcquitty`", "`median`" or "`centroid`".
`margins`	A numeric vector of length 2 containing the margins for group and metabolite names, respectively.
`key`	A logical indicating whether a colour key must be drawn.
`keysize`	A numeric indicating the size of the key.
`cexRow`	A numeric indicating the size of the metabolite names.
`ColSideColors`	A character vector indicating the colours different groups.
`...`	Arguments to be passed on to other methods.

Alysha M De Livera, Gavriel Olshansky

par, heatmap.2.

    data(mixdata)  #unadjusted data
    HeatMap(mixdata$featuredata,mixdata$sampledata[,1], 
             saveplot = FALSE, 
            interactiveplot = TRUE, scale = "row", 
            dendrogram = "none", colramp=c(75,"magenta","green"))