ecdfquantileplot: ECDF plot of a given quantile of a variable calculated by...

In DRomics: Dose Response for Omics

ECDF plot of a given quantile of a variable calculated by group

Description

Plots a given quantile of a variable calculated by group as an ECDF plot with points sized by the numbers of items per group. In the context of this package this function is intended to be used with the BMD as the variable and with groups defined by the user from functional annotation.

Usage

ecdfquantileplot(variable, by, quantile.prob = 0.5, title)

Arguments

variable	A numeric vector corresponding to the variable on which we want to calculate the given quantile by group. In the context of the package this variable may be a BMD.
by	A factor of the same length defining the groups. In the context of this package this factor may code for groups defined by the user from functional annotation.
quantile.prob	The probability (in ]0, 1[) defining the quantile to calculate on each group.
title	An optional title for the plot.

Details

The given quantile is calculated for each group (e.g.from all items of a metabolic pathway) using function quantile and plotted as an ECDF plot. In this ECDF plot of quantiles each point is sized according to the number of items in the corresponding group (e.g. metabolic pathway). We recommend the use of the new function sensitivityplot that may be more convenient and that offers more options.

Value

a ggplot object.

Author(s)

Marie-Laure Delignette-Muller

See Also

See quantile and sensitivityplot.

Examples

# (1) An example from data published by Larras et al. 2020
# in Journal of Hazardous Materials
# https://doi.org/10.1016/j.jhazmat.2020.122727

# a dataframe with metabolomic results (output $res of bmdcalc() or bmdboot() functions)
resfilename <- system.file("extdata", "triclosanSVmetabres.txt", package="DRomics")
res <- read.table(resfilename, header = TRUE, stringsAsFactors = TRUE)
str(res)

# a dataframe with annotation of each item identified in the previous file
# each item may have more than one annotation (-> more than one line)
annotfilename <- system.file("extdata", "triclosanSVmetabannot.txt", package="DRomics")
annot <- read.table(annotfilename, header = TRUE, stringsAsFactors = TRUE)
str(annot)

# Merging of both previous dataframes
# in order to obtain an extenderes dataframe
# bootstrap results and annotation
annotres <- merge(x = res, y = annot, by.x = "id", by.y = "metab.code")
head(annotres)

### an ECDFplot of quantiles of BMD-zSD calculated by pathway
ecdfquantileplot(variable = annotres$BMD.zSD, 
               by = annotres$path_class,
               quantile.prob = 0.25) 
 
# same plot in log10 dose scale (not interesting on this example
# but could be on another one) 
if (require(ggplot2))
  ecdfquantileplot(variable = annotres$BMD.zSD, 
               by = annotres$path_class,
               quantile.prob = 0.25) + scale_y_log10() 

DRomics documentation built on Oct. 16, 2024, 5:09 p.m.