plotHeatmapH: Heatmap corresponding to h-statistic matrix provided by DECO...

In fjcamlab/deco: Decomposing Heterogeneous Cohorts using Omic Data Profiling

Heatmap corresponding to h-statistic matrix provided by DECO analysis.

Description

This function returns three plots showing the association among different sample subclasses found by DECO and any sample information of interest. This information can be the initial classes or any new included sample information.

Usage

plotHeatmapH(deco, info.sample = NA, info.feature = NA, 
      print.annot = FALSE, cex.legend = 1, 
      cex.names = 1)

Arguments

deco	a "deco" R object generated by 'decoNSCA' R function.
info.sample	a data.frame with relevant information of samples to be plot on 'Heatmap'.
info.feature	a data.frame with relevant information of genes or features to be plot on 'Heatmap'.
print.annot	logical indicating if annotation (gene SYMBOL) should be printed instead original IDs. This option needs previous annotation within 'decoRDA' function or late annotation binding information to @featureTable slot of 'deco' R object.
cex.legend	numerical value giving the amount of magnification of legend.
cex.names	numerical value giving the amount of magnification to gene names or sample names.

Details

Heatmap plot showing h-statistic matrix (H) and biclustering of features-samples.

Value

A customized heatmap plot showing h-statistic matrix and biclustering of features-samples.

Author(s)

Francisco Jose Campos Laborie. <[e-mail]>

See Also

decoReport, decoNSCA

Examples

#### Further information in DECO vignette(s).
## Run after decoRDA and decoNSCA steps on 'ALCLdata'
data(ALCLdata)
ALCL

### Phenotype information
info.sample <- as.data.frame(colData(ALCL))[,8:9]
rownames(info.sample) <- rownames(colData(ALCL))

#### Heatmap with h-statistic matrix and biclustering of features-samples.
## Not run as example
# plotHeatmapH(deco = deco.results.ma, info.sample = info.sample, 
#              cex.names = 0.3, print.annot = FALSE)

fjcamlab/deco documentation built on Aug. 18, 2024, 4:28 a.m.