PlotSubHeatMap: Plot heatmap

In flajole/MApckg: R package of MetaboAnalyst functions

Description

Plot a sub heatmap based on results from t-tests/ANOVA, VIP or Random Forest analysis. Uses pheatmap function. Heatmap provides intuitive visualization of the data table. 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.
Tip 1: Do not re-organize samples/rows to show the natural contrast among groups (with each group a block).
Tip 2: Display top number of features ranked by t-tests to retain the most constrasting patterns.

Usage

PlotSubHeatMap(dataSet, analSet, imgName = "heatmap_", format = "png",
  dpi = 72, width = NA, smplDist = "euclidean", clstDist = "ward.D",
  colors = "default", method.nm = "tanova", top.num = 25,
  viewOpt = "overview", rowV = TRUE, colV = TRUE, border = T)

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"
method.nm	Type of analysis applied to detect features with the best contrast. One of "tanova" - for t-test or ANOVA; "vip" - for PLS-DA VIP; "rf" - for Random Forest analysis
top.num	The number of the features with the best contrast to be plotted.
viewOpt	View mode, "overview" or "detailed"
rowV	If TRUE, samples are reorganized.
colV	If TRUE, features are reorganized.
border	If TRUE, show cell borders.

Value

Native analSet with one added $htmap element containing:

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

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

See Also

pheatmap for used statistical function
PlotHeatMap2 for two-factored data

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