drawHeatmap: Generate heatmaps

Description Usage Arguments Details Value Author(s) References Examples

View source: R/Valiation.R

Description

Generate heatmap for datasets.

Usage

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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 taosheng.x@gmail.com,Thuc Le Thuc.Le@unisa.edu.au

References

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

Examples

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### 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")

xtsvm/CancerSubtypes documentation built on May 4, 2019, 1:26 p.m.