get_pcascoredistplots: get_pcascoredistplots

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

Description

PCA score distribution (25th percentile, median, 75th percentile) plots

Usage

get_pcascoredistplots(X = NA, Y = NA, feature_table_file, parentoutput_dir,
class_labels_file, sample.col.opt = "rainbow", plots.width = 2000,
plots.height = 2000, plots.res = 300, alphacol = 0.3, col_vec,
pairedanalysis = FALSE, pca.cex.val = 3, legendlocation = "topright",
pca.ellipse = TRUE, ellipse.conf.level = 0.5, filename = "all")

Arguments

X	R object for feature table. If this is given, then feature table can be set to NA.
Y	R object for response/class labels matrix. If this is given, then class labels file can be set to NA.
feature_table_file	Path and name of 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. If you want to adjust for covariates in "lmreg" option, then you can add additional columns, one per covariate. Categorical variables should be strings (eg: "male", "female"). Please see "classlabels_gender.txt" file as an example.
sample.col.opt	Color scheme for PCA and heatmap sample axis eg: "rainbow", "heat" or "topo"
alphacol	Color scaling parameter eg:0.3
col_vec	Vector of colors for each sample.
pairedanalysis	Is this a paired-study design? TRUE or FALSE If samples are paired, then the feature table and the class labels file should be organized so that the paired samples are arranged in the same order in each group. For example, the first sample in group A and the first sample in group B should be paired.
pca.cex.val	Size of points on PCA plots. eg: 4
legendlocation	Legend location on PCA plots
pca.ellipse	Should ellipse be plotted on PCA plots? eg: TRUE or FALSE
ellipse.conf.level	Confidence interval for PCA ellipses eg: 0.95
filename	Name of output PDF file

Details

This function performs PCA and generates pariwise score plots as well as score distribution plots (per group). It uses the Y vector and classlabels for color coding the samples in the pairwise score plots.

Value

The output includes: Pairwise PCA score plots, PCA score distribution plots, PCA scores and loadings text files.

Note

The plots can be sent to an external device by running the following commands: pdf("get_pcascoredistplots.pdf") get_pcascoredistplots(...) dev.off()

Author(s)

Karan Uppal

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