get_boxplots: get_boxplots

In kuppal2/xmsPANDA: R Package for Biomarker Discovery, Network, and Data Exploratory Analysis

Description

This function generates boxplots for m/z features. The input intensity matrix could be transformed or non-transformed intensities. Sample labels in the class labels file should be in the same order as the intensity matrix or feature table.

Usage

get_boxplots(feature_table_file, parentoutput_dir, class_labels_file, sample.col.opt = "rainbow", plots.width = 2000, plots.height = 2000, plots.res = 300, alphacol = 0.3)

Arguments

feature_table_file	Feature table that includes the mz, retention time, and measured intensity in each sample for each analyte. The first 2 columns should be the mz and time. The remaining columns should correspond to the samples in the class labels file with each column including the intensity profile of a sample. Full path required. Eg: C:/My Documents/test.txt The feature table should be in a tab-delimited format. An example of the input file is provided under the "example" folder.
parentoutput_dir	Provide full path of the folder where you want the results to be written. Eg: C:/My Documents/ProjectA/results/
class_labels_file	File with class labels information for each sample. Samples should be in the same order as in the feature table. Please use the same format as in the example folder.
sample.col.opt	Color scheme for PCA and heatmap sample axis eg: "heat" or "topo"
alphacol=0.3	Color scaling parameter eg:0.3

Value

Creates a PDF with boxplots for each m/z feature.

Author(s)

Karan Uppal <[e-mail]>

kuppal2/xmsPANDA documentation built on May 15, 2021, 5:48 a.m.