bar_update_manual: Plots the relative amounts of the metabolites that are part...

In juyeki/MetabR: Functions to assist in the current UCLA Metabolomics Quality Control and Analysis Pipeline.

Description

This function takes in the pathway of interest, a data frame containing the relative amounts of the different metabolites in the experiment, the number of conditions in the experiment, and the type of analysis or quality control being run. This function returns a page of plots of the relative amounts of the different metabolites that are part of the specified defined pathway ('metabolites' parameter)

Usage

bar_update_manual(metabolites = 'glycolysis', df = data4, n = num_conditions, type = "250k")

Arguments

metabolites	The metabolic pathway to be plotted. Pathways that are pre-defined internally include 'glycolysis', 'TCA', 'PPP', 'Curr', 'Cys', 'Adenine', 'Cytosine', 'Guanine', 'Thymine', 'Uracil', 'AA', 'Hex', 'FA', 'Fru', 'CoAs', and 'Neurotrans'. A custom vector of metabolites of interest can also be passed in to the function.
df	A dataframe containing the data on the relative amounts of the different metabolites in the analysis.
n	The number of conditions in the experiment.
type	The type of analysis or quality control being run. For 250K and blanks quality control, type should be set to '250k'. The default 'type' works correctly for the blanks quality control plots.
index	A list of two vectors, the first one containing the indices of the 250Ks and the second one containing the indices of the blanks.
title_type	The type of manually entered metabolite group that is being plotted. For medium metabolite plots, title_type should be set to 'medium'. For nonpathway metabolites, the title_type should be set to 'nonpathway.'
only_M0	Optional parameter. A vector of the metabolites that were only measured in M0 and that shouldn't be included in the Isotopologue Distribution, Percent Labelled, or Fractional Contribution plots.

Author(s)

Gerardo Javier, Daniel Tan, Jordan Uyeki

juyeki/MetabR documentation built on Aug. 6, 2020, 3:32 a.m.