build_sortHeatmap: Build the heatmap matrices

In MineICA: Analysis of an ICA decomposition obtained on genomics data

Description

This function returns the matrices that will be used to plot the heatmaps of each component. It restricts the data matrix of the icaSet object to the contributing genes/features, and order the features/genes and samples.

Usage

  build_sortHeatmap(icaSet, selCutoff, selectionByComp,
    level = c("features", "genes"), samplesOrder,
    featuresOrder)

Arguments

icaSet	The IcaSet object
selCutoff	The threshold used to select the contributing features/genes based on their projection values. Must be either of length 1 and the same treshold is applied to all components, or of length equal to the number of components and one specific threshold is used for each component.
selectionByComp	The list of gene projections per components already restricted to the contributing genes
level	A character indicating which data level is used to plot the heatmaps: 'features' to plot measured feature levels (e.g probe sets expression values), 'genes' to plot measured gene values (e.g gene expression values).
samplesOrder	A list providing the order of the samples, per component, to be used in the heatmaps. If NULL, the contribution values of the samples are used to rank the columns of the heatmaps.
featuresOrder	A list providing the features or genes order, per component, to be used in the heatmaps. If NULL, the projection values of the genes are used to rank the rows of the heatmaps.

Details

This function is called by function plot_heatmapsOnSel and is not likely to be called alone.

Value

A list of matrices

Author(s)

Anne Biton

MineICA documentation built on Nov. 8, 2020, 5:35 p.m.