hc_logFC_DensityPlot: Density plots of logFC values

In samWieczorek/DAPAR: Tools for the Differential Analysis of Proteins Abundance with R

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)

samWieczorek/DAPAR documentation built on May 6, 2022, 5:30 p.m.