classes_pca: PCA plot visualising pathway-based classification of samples...

In a-thind/PathAnalyser: ER & HER2 Pathway Activity Analysis For Breast Cancer Transcriptomic Datasets

PCA plot visualising pathway-based classification of samples in a dataset

Description

This function generates a PCA plot showing the clustering of samples in the normalised expression data set, coloured by predicted pathway activity labels: active (green), inactive (orange) and uncertain (blue). An ideal pathway-based classification would generate a PCA plot showing tight clustering of samples in each activity class and less overlap between classes.

Usage

classes_pca(norm_data, predicted_labels_df, pathway = "Pathway Activity")

Arguments

norm_data	A (logCPM) normalized gene expression data matrix, with row names consisting of the HUGO gene symbols and column names corresponding to the name / ID of each sample in the dataset
predicted_labels_df	A data frame containing the pathway activity labels predicted by classification algorithm for each sample in the dataset. The first column is called "sample" which contains the sample names in the data set and the second column is called "class" containing the corresponding predicted pathway activity of the sample.
pathway	The pathway name used in the title of the plot, default is a placeholder "Pathway Activity".

Author(s)

Yi-Hsuan Lee [e-mail]

Examples

## Not run: classes_pca(norm_data, predicted_labels_df, 'ER')

a-thind/PathAnalyser documentation built on May 6, 2022, 9:50 a.m.