hc_logFC_DensityPlot: Density plots of logFC values

In prostarproteomics/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

data(Exp1_R25_prot, package="DAPARdata")
obj <- Exp1_R25_prot[seq_len(100)]
level <- 'protein'
metacell.mask <- match.metacell(GetMetacell(obj), c("Missing POV", "Missing MEC"), 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")
pal <- ExtendPalette(2, "Dark2")
hc_logFC_DensityPlot(res$logFC, threshold_LogFC = 1, pal = pal)

prostarproteomics/DAPAR documentation built on March 28, 2024, 4:44 a.m.