drawHeatmap {CancerSubtypes} | R Documentation |
Generate heatmap for datasets.
drawHeatmap(data, group = NULL, silhouette = NULL, scale = "no", labRow = NULL, labCol = NULL, color = colorRampPalette(c("green", "black", "red"))(300), Title = NA)
data |
A matrix representing the genomic data such as gene expression data, miRNA expression data. |
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:
|
labRow |
labels for the rows. Possible values are:
|
labCol |
labels for the columns. See labRow. |
color |
color specification for the heatmap. |
Title |
A string for the Main title of the heatmap. |
We applied the R package "NMF" function "aheatmap()" as the heatmap drawer.
A heatmap
Xu,Taosheng taosheng.x@gmail.com,Thuc Le Thuc.Le@unisa.edu.au
Gaujoux, Renaud, and Cathal Seoighe. "A flexible R package for nonnegative matrix factorization." BMC bioinformatics 11.1 (2010): 1.
### 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")