plot_parallel: Parallel coordinates plot of expression data

In jcalendo/coriell: Convenience Functions for Bioinformatics

Parallel coordinates plot of expression data

Description

The parallel coordinates plot will display a line plot showing the expression value for gene on the y-axis by each sample on the x-axis.

Usage

plot_parallel(x, ...)

## Default S3 method:
plot_parallel(x)

## S3 method for class 'matrix'
plot_parallel(x, metadata = NULL, colBy = NULL, removeVar = NULL, ...)

## S3 method for class 'data.frame'
plot_parallel(x, metadata = NULL, colBy = NULL, removeVar = NULL, ...)

## S3 method for class 'SummarizedExperiment'
plot_parallel(x, assay = "counts", colBy = NULL, removeVar = NULL, ...)

Arguments

x	gene by sample matrix or SummarizedExperiment object
...	Additional parameters passed to ggplot2::geom_line()
metadata	data.frame containing metadata per sample. rownames of metadata
colBy	metadata column used to color lines. Default NULL, every sample will get its own color.
removeVar	Remove this proportion of features based on the variance across rows. Default NULL, all features are plotted.
assay	assay of SummarizedExperiment object to be plotted. Default "counts".

Value

ggplot object

Examples

# Create metadata for plotting
metadata <- data.frame(row.names = colnames(GSE161650_lc))
metadata$Group <- rep(c("DMSO", "THZ1"), each = 3)

# Plot the PCP for each sample -- passing alpha value to geom_line()
plot_parallel(GSE161650_lc, alpha = 0.01)

# Plot the PCP by coloring each sample by Group from metadata
plot_parallel(GSE161650_lc, metadata, colBy = "Group", alpha = 0.01)

jcalendo/coriell documentation built on March 5, 2025, 5:42 a.m.