drawHeatmap: Generate heatmaps

In CancerSubtypes: Cancer subtypes identification, validation and visualization based on multiple genomic data sets

Description

Generate heatmap for datasets.

Usage

drawHeatmap(data, group = NULL, silhouette = NULL, scale = "no",
  labRow = NULL, labCol = NULL, color = colorRampPalette(c("green",
  "black", "red"))(300), Title = NA)

Arguments

data	A matrix representing the genomic data such as gene expression data, miRNA expression data. For the matrix, the rows represent the genomic features, and the columns represent the samples.
group	A vector representing the subtype on each sample. The default is NULL. If it is not NULL, the samples will be rearrangement according to the subtypes in the heatmap.
silhouette	An object of class silhouette. It is a result from function silhouette() or silhouette_SimilarityMatrix(). The default is NULL. If it is not NULL, an annotation will be drawn to show the silhouette width for each sample.
scale	A string for data normalization type before heatmap drawing. The optional values are shown below: "no". No normalization. This is default. "z_score". Normalize data by z_score of features. "max_min". Normalize each feature by (value-min)/(max-min).
labRow	labels for the rows. Possible values are: NULL. The default value. It will use the row names of the matrix for the heatmap labels. NA. No row label will be shown. A list of labels.
labCol	labels for the columns. See labRow.
color	color specification for the heatmap.
Title	A string for the Main title of the heatmap.

Details

We applied the R package "NMF" function "aheatmap()" as the heatmap drawer.

Value

A heatmap

Author(s)

Xu,Taosheng [e-mail],Thuc Le [e-mail]

References

Gaujoux, Renaud, and Cathal Seoighe. "A flexible R package for nonnegative matrix factorization." BMC bioinformatics 11.1 (2010): 1.

Examples

### SNF result analysis
data(GeneExp)
data(miRNAExp)
data(time)
data(status)
GBM=list(GeneExp=GeneExp,miRNAExp=miRNAExp)
result=ExecuteSNF(GBM, clusterNum=3, K=20, alpha=0.5, t=20)
group=result$group
distanceMatrix=result$distanceMatrix
silhouette=silhouette_SimilarityMatrix(group, distanceMatrix)
drawHeatmap(GeneExp,group,silhouette=silhouette,scale="max_min",Title="GBM Gene Expression")
drawHeatmap(GeneExp,group,silhouette=silhouette,scale="max_min",
            color="-RdYlBu",Title="GBM Gene Expression")

Example output

Loading required package: sigclust
Loading required package: NMF
Loading required package: pkgmaker
Loading required package: registry
Loading required package: rngtools
Loading required package: cluster
NMF - BioConductor layer [OK] | Shared memory capabilities [OK] | Cores 2/2
Warning message:
In SNFtool::SNF(W_temp, K = K, t = t) :
  Dim names not consistent across all matrices in Wall.
            Returned matrix will have no dim names.

CancerSubtypes documentation built on Nov. 8, 2020, 8:24 p.m.