PlotHeatMap2: Plot two-factor heatmap

In flajole/MApckg: R package of MetaboAnalyst functions

Description

Uses pheatmap function. This method displays data in the form of colored cells. It provides direct visualization of the relative levels of individual samples or variables. Each colored cell on the map corresponds to a concentration value in your data table, with samples in rows and features/compounds in columns. You can use heatmap to identify samples/features that are unusually high/low.

Usage

PlotHeatMap2(dataSet, analSet, imgName = "heatmap2_", format = "png",
  dpi = 72, width = NA, smplDist = "euclidean", clstDist = "average",
  colors = "default", viewOpt = "overview", hiRes = FALSE,
  sortInx = "B", var.inx = 1:ncol(dataSet$norm))

Arguments

dataSet	List, data set object generated by MS_to_MA function.
analSet	List, containing the results of statistical analysis (can be just an empty list).
imgName	Image file name prefix.
format	Image format, one of: "png", "tiff", "pdf", "ps", "svg"
dpi	Image resolution.
width	Image width.
smplDist	The distance measure, one of "euclidean", "pearson", "minkowski"
clstDist	The agglomeration method to be used, one of "ward.D", "ward.D2", "single", "complete", "average". For details: pheatmap
colors	The color contrast. One of "default", "gbr" (red/green), "heat", "topo", "gray"
viewOpt	View mode, "overview" or "detailed"
hiRes	If TRUE, then produces hi-resolution plot.
sortInx	If "A", samples are arranged by the first factor; if "B" - by the second one.
var.inx	Vector of the numbers of plotted features.

Value

Native analSet with one added $htmap2 element containing:

• $htmap2$dist.par - equal smplDist argument value

• $htmap2$clust.par - equal clstDist argument value

See Also

pheatmap for used statistical function
PlotSubHeatMap for one-factored data

flajole/MApckg documentation built on May 16, 2019, 1:16 p.m.