In eckartbindewald/bfxapps2: R Bioinformatics Applications
knitr::opts_chunk$set(echo = FALSE)
Visualizing taxonomic abundances with heat trees
library(metacoder)
library(RColorBrewer)
remote_dir="https://raw.githubusercontent.com/PacktPublishing/R-Bioinformatics-Cookbook/master"
biom_file <- file.path(remote_dir, "datasets", "ch5", "rich_high_count_otu.biom")
taxdata <- parse_qiime_biom(biom_file)
str(taxdata)
Visualization
heat_tree(taxdata, node_label = taxon_names, node_size = n_obs, node_color = n_supertaxa, layout = "gem", title = "sample heat tree", node_color_axis_label = "Number of Supertaxa", node_size_axis_label = "Number of OTUs", node_color_range = brewer.pal(5, "Greens"))
eckartbindewald/bfxapps2 documentation built on Feb. 6, 2025, 3:22 a.m.
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knitr::opts_chunk$set(echo = FALSE)
Visualizing taxonomic abundances with heat trees
library(metacoder) library(RColorBrewer) remote_dir="https://raw.githubusercontent.com/PacktPublishing/R-Bioinformatics-Cookbook/master" biom_file <- file.path(remote_dir, "datasets", "ch5", "rich_high_count_otu.biom") taxdata <- parse_qiime_biom(biom_file) str(taxdata)
Visualization
heat_tree(taxdata, node_label = taxon_names, node_size = n_obs, node_color = n_supertaxa, layout = "gem", title = "sample heat tree", node_color_axis_label = "Number of Supertaxa", node_size_axis_label = "Number of OTUs", node_color_range = brewer.pal(5, "Greens"))
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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