metHeatmap: Heatmap

In ethevenot/metabolis: Metabolomics Data Analysis

Description

Heatmap of a MultiDataSet instance

Heatmap of an ExpressionSet instance

Usage

metHeatmap(x, ...)

## S4 method for signature 'MultiDataSet'
metHeatmap(x, fig.pdfC = NA, info.txtC = NA,
  ...)

## S4 method for signature 'ExpressionSet'
metHeatmap(x, dissymC = c("euclidean",
  "maximum", "manhattan", "canberra", "binary", "minkowski", "1-cor",
  "1-abs(cor)")[7], correlC = c("pearson", "kendall", "spearman")[1],
  aggloC = c("ward.D", "ward.D2", "single", "complete", "average",
  "mcquitty", "median", "centroid")[2], clustVi = c(2, 2),
  fig.pdfC = NA, plotCexVn = c(1, 1),
  plotPaletteC = c("blueOrangeRed", "redBlackGreen")[1],
  plotScaleL = TRUE, info.txtC = NA)

Arguments

x	an S4 object of class MultiDataSet
...	additional parameters (see the documentation)
fig.pdfC	Character: Name of the file for the graphics from the significant features; if NA, the graphics are displayed on the screen;
info.txtC	Character: File name for the printed results (call to 'sink()'); if NA (default), messages will be printed on the screen; if NULL, no verbose will be generated
dissymC	Character: [hclust]
correlC	Character: correlation coefficient (in case '1-cor' or '1-abs(cor)' are selected as dissymilarity)
aggloC	charcter: agglomeration method
clustVi	tupple of integers: number of sample and variable clusters, respectively
plotCexVn	vector of numerics:
plotPaletteC	character: color palette
plotScaleL	logical: scaling (mean-centering and unit variance scaling) to enhance contrast (for plotting only)
x	An S4 object of class ExpressionSet
fig.pdfC	Character: Name of the file for the graphics from the significant features; if NA, the graphics are displayed on the screen;
info.txtC	Character: File name for the printed results (call to 'sink()'); if NA (default), messages will be printed on the screen; if NULL, no verbose will be generated

Value

MultiDataSet including the column with the cluster numbers in pData and fData

ExpressionSet including the adjusted p-values in fData (or the vector of adjusted p-values when returnAdjustOnlyL is TRUE)

Examples

prometMset <- metRead(system.file("extdata/promet/",
package="metabolis"))
prometMset <- metHeatmap(prometMset)
sacSet <- metRead(system.file("extdata/sacurine",
package="metabolis"))
sacSet <- metTransform(sacSet, "log10")
sacSet <- metHeatmap(sacSet)
head(fData(sacSet))

ethevenot/metabolis documentation built on June 28, 2019, 1:27 p.m.