plot_samples_with_low_median_metabolites: Show how many samples have low measurements in how many...

In cbhelmholtz/metaboliteqc: metaboliteqc --- Quality controling metabolite data

Description

Plot the number of samples for which a given number of groups has mean metabolite measurements below a given percentile.

Usage

plot_samples_with_low_median_metabolites(mat, by, percentiles,
  by_label = NULL, xlim = NULL, ylim = NULL, main = NULL)

Arguments

mat	Matrix with samples as columns and metabolites as rows
by	Factor of length nrow(mat) used to group rows
percentiles	Integer vector with numbers between 0 and 100.
by_label	Label used in plot annotations to refer to the groups defined by by
xlim	Limits plotting range on x-axis
ylim	Limits plotting range on y-axis
main	Title

Details

Algorithm: For every sample and every group of rows the mean metabolite measurement is computed. This results in every sample having one value per group (the mean metabolite measurement). We then count for every sample the number of groups in which the sample's mean metabolite measurement is less that or equal to the given percentile of the distribution of all mean metabolite measurements in that group. Finally we plot the number of groups N against the number of samples with mean metabolite measurements less than or equal to the given percentile in N groups.

Value

Returns NULL invisibly.

cbhelmholtz/metaboliteqc documentation built on May 13, 2019, 2:03 p.m.