mrheatmap: A function for plotting heatmaps.

In mrbin: Metabolomics Data Analysis Functions

A function for plotting heatmaps.

Description

This function plots heatmaps based on rank order, using heatmap from the stats package

Usage

mrheatmap(
  results,
  binlist = NULL,
  samplelist = NULL,
  annotate = FALSE,
  cexRow = 0.7,
  cexCol = 0.8,
  margins = c(4, 6),
  Colv = NA,
  Rowv = NULL,
  closeDevice = TRUE,
  ...
)

Arguments

results	Either an mrbin object or a numeric matrix containing sample names as rownames and feature names as columns names.
binlist	A vector containing bin names as they are generated by mrbin (colnames). If provided, only these columns will be shown.
samplelist	A vector containing sample names (rownames). If provided, only these rows will be shown.
annotate	Should peak annotations be shown? This requires annotation data in the mrbin object.
cexRow	Font size for row labels
cexCol	Font size for column labels
margins	Determines the plot margins.
Colv	Determines if and how the column dendrogram should be computed and reordered. Default: NA (dendrogram will not be used)
Rowv	Determines if and how the row dendrogram should be computed and reordered. Default: NULL (dendrogram will be used)
closeDevice	Should previous plots be closed prior to plotting?
...	Additional graphical parameters that will be passed to the stats function heatmap

Value

None

Examples

resetEnv()
# First create NMR bin data, then plot some differential bins.
results<-mrbin(silent=TRUE,setDefault=TRUE,parameters=list(verbose=FALSE,
                dimension="1D",binwidth1D=0.01,PCA="No",showSpectrumPreview="No",
                signal_to_noise1D=25,noiseThreshold=0.75,useAsNames="Spectrum titles",
                NMRfolders=c(
                system.file("extdata/1/10/pdata/10",package="mrbin"),
                system.file("extdata/2/10/pdata/10",package="mrbin"),
                system.file("extdata/3/10/pdata/10",package="mrbin"))
                ))
metadata<-c(0,0,1)
#Find significant signals
pvalues<-rep(NA,ncol(results$bins))
names(pvalues)<-colnames(results$bins)
for(i in 1:ncol(results$bins)){
	model<-stats::lm(intensity~treatment, 
     data=data.frame(intensity=results$bins[,i],treatment=metadata))
	pvalues[i]<-stats::anova(model)$"Pr(>F)"[1]
}
significantBins<-names(sort(pvalues)[1:30]) 
metaboliteIdentities=matrix(c(1.346,1.324,21,23,
                              4.12,4.1,70.8578,71.653,
                              3.052,3.043,30.5,33.5,
                              4.066,4.059,57,59.5,
                              5.7,6.0,0,150),
                   ncol=4,byrow=TRUE)
#Annotate the dataset with signal identities
rownames(metaboliteIdentities)=c("Lactate","Lactate","Creatinine","Creatinine","Urea")
results<-annotatemrbin(results,metaboliteIdentities=metaboliteIdentities)
mrheatmap(results=results,
    binlist=significantBins,annotate=TRUE,
    main="Significant signals")

mrbin documentation built on April 4, 2025, 5:24 a.m.