plot_pcoa: plot_pcoa

In OxfordCMS/OCMSutility: Utility functions for OCMS

plot_pcoa

Description

This is a simple PCoA function that colours all points by one metadata variable. It can be helpful to visualise metadata variables independently when assessing potential confounding metadtaa factors

Usage

plot_pcoa(relab, met, colour = NULL, shape = NULL, CI = 0.95)

Arguments

relab	dataframe. relative abundance data with features in rows and samples in columns. feature IDs in rowname.
met	dataframe. metadata with samples in rows. sample IDs in rowname
colour	string. defulat NULL. metadata variable to colour points by
shape	string. default NULL. metadata variable to set shape of points by
CI	numeric. Default 0.95. Confidence interval used to draw ellipse around colour variable. set to NULL to omit drawing ellipse

Examples

data(dss_example)
met_df <- dss_example$metadata

count_df <- dss_example$merged_abundance_id %>%
  column_to_rownames('featureID')
count_df <- count_df[,met_df$sampleID]
relab <- relab(count_df)

iter_var <- c('Genotype','Phenotype')
for(i in iter_var) {
  plot_pcoa(relab, met_df, colour = i)
}

OxfordCMS/OCMSutility documentation built on Feb. 27, 2025, 8:19 p.m.