PlotProbView: Plot a summary view of the classification result

In xia-lab/MetaboAnalystR: An R Package for Comprehensive Analysis of Metabolomics Data

Plot a summary view of the classification result

Description

Plot of predicted class probabilities. On the x-axis is the proability, and the y-axis is the index of each predicted sample based on the probility. The samples are turned into separations at the x-axis. This plot can be created for multivariate ROC curve analysis using SVM, PLS, and RandomForest. Please note that sometimes, not all samples will be tested, instead they will be plotted at the 0.5 neutral line.

Usage

PlotProbView(mSetObj=NA, imgName, format="png", dpi=72, mdl.inx, show, showPred)

Arguments

mSetObj	Input the name of the created mSetObj (see InitDataObjects)
imgName	Input a name for the plot
format	Select the image format, "png", of "pdf".
dpi	Input the dpi. If the image format is "pdf", users need not define the dpi. For "png" images, the default dpi is 72. It is suggested that for high-resolution images, select a dpi of 300.
mdl.inx	Model index, 0 means to compare all models, -1 means to use the best model, input 1-6 to plot a ROC curve for one of the top six models
show	1 or 0, if 1, label samples classified to the wrong groups
showPred	Show predicted samples

Author(s)

Jeff Xia [e-mail] McGill University, Canada License: GNU GPL (>= 2)

xia-lab/MetaboAnalystR documentation built on April 20, 2024, 8:13 p.m.