GeneHeatmap {ILoReg} | R Documentation

## Heatmap visualization of the gene markers identified by FindAllGeneMarkers

### Description

The GeneHeatmap function enables drawing a heatmap of the gene markers identified by FindAllGeneMarkers, where the cell are grouped by the clustering.

### Usage

    GeneHeatmap.SingleCellExperiment(object, clustering.type, gene.markers)

    ## S4 method for signature 'SingleCellExperiment'
    GeneHeatmap(object, clustering.type = "manual", gene.markers = NULL)

### Arguments

`object` | of `SingleCellExperiment` class
`clustering.type` | "manual" or "optimal". "manual" refers to the clustering formed using the "SelectKClusters" function and "optimal" to the clustering using the "CalcSilhInfo" function. Default is "manual".
`gene.markers` | a data frame of the gene markers generated by FindAllGeneMarkers function. To accelerate the drawing, filtering the dataframe by selecting e.g. top 10 genes is recommended.

### Value

nothing

### Examples

    library(SingleCellExperiment)
    sce <- SingleCellExperiment(assays = list(logcounts = pbmc3k_500))
    sce <- PrepareILoReg(sce)
    ## These settings are just to accelerate the example, use the defaults.
    sce <- RunParallelICP(sce,L=2,threads=1,C=0.1,r=1,k=5) # Use L=200
    sce <- RunPCA(sce,p=5)
    sce <- HierarchicalClustering(sce)
    sce <- SelectKClusters(sce,K=5)
    gene_markers <- FindAllGeneMarkers(sce,log2fc.threshold = 0.5,min.pct = 0.5)
    top10_log2FC <- SelectTopGenes(gene_markers,top.N=10,
    criterion.type="log2FC",inverse=FALSE)
    GeneHeatmap(sce,clustering.type = "manual",
     gene.markers = top10_log2FC)

[Package ILoReg version 1.0.0 Index]