plotGainingH {deco} | R Documentation

## Gaining plots for using h-statistic instead original omic data.

### Description

This function returns three plots for a particular feature(s), showing the correlation between the h-statistic calculated by DECO and the original omic data.

### Usage

    plotGainingH(deco, data, ids, print.annot = FALSE,
                 orig.classes = TRUE)

### Arguments

`deco` | a "deco" R object generated by 'decoNSCA' R function.
`data` | a matrix of normalized omic data with 'f' features (rows) by 'n' samples (columns).
`ids` | character vector indicating what original IDs from input data should be highlighted and plot in 'Profile' section. If all IDs found have to be plot, input all corresponding IDs here.
`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.
`orig.classes` | logical indicating if original sample categories compared (orig.classes = TRUE) or DECO subclasses (orig.classes = FALSE) will be represented.

### Details

Diagnostic plot associating omic profile and h-statistic profile of any significant feature found by DECO.

### Value

Three plots are returned: Boxplot: distribution of omic data and h-statistic values per DECO subclass. Top-left: parametric correlation between omic data and h-statistic per sample. Top-right: non-parametric correlation (ranking) between omic data and h-statistic per sample.

### Author(s)

Francisco Jose Campos Laborie. <fjcamlab@gmail.com>

### See Also

`decoRDA`, `decoNSCA`

### Examples

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

    ## Feature to represent
    id <- featureTable(deco.results.ma)[1, "ID"]

    #### Comparing DECO subclasses against source of samples.
    plotGainingH(deco.results.ma, data = assay(ALCL), ids = id,
                 print.annot = FALSE, orig.classes = FALSE)

[Package deco version 1.4.1 Index]