hc_logFC_DensityPlot {DAPAR} | R Documentation

## Density plots of logFC values

### Description

This function show the density plots of Fold Change (the same as calculated by limma) for a list of the comparisons of conditions in a differential analysis.

### Usage

    hc_logFC_DensityPlot(df_logFC, threshold_LogFC = 0, pal = NULL)

### Arguments

`df_logFC` | A dataframe that contains the logFC values
`threshold_LogFC` | The threshold on log(Fold Change) to distinguish between differential and non-differential data
`pal` | xxx

### Value

A highcharts density plot

### Author(s)

Samuel Wieczorek

### Examples

    utils::data(Exp1_R25_prot, package='DAPARdata')
    obj <- Exp1_R25_prot[1:1000]
    level <- obj@experimentData@other$typeOfData
    metacell.mask <- match.metacell(GetMetacell(obj), 'missing', level)
    indices <- GetIndices_WholeMatrix(metacell.mask, op='>=', th=1)
    obj <- MetaCellFiltering(obj, indices, cmd='delete')
    qData <- Biobase::exprs(obj$new)
    sTab <- Biobase::pData(obj$new)
    res <- limmaCompleteTest(qData, sTab, comp.type = "OnevsAll")
    hc_logFC_DensityPlot(res$logFC, threshold_LogFC=1)
    pal <- ExtendPalette(2, 'Dark2')
    hc_logFC_DensityPlot(res$logFC, threshold_LogFC=1, pal=pal)

[Package DAPAR version 1.24.8 Index]