plot_orthofinder_stats: Plot a panel with a summary of Orthofinder stats

In almeidasilvaf/cogeqc: Systematic quality checks on comparative genomics analyses

Plot a panel with a summary of Orthofinder stats

Description

This function is a wrapper for plot_species_tree, plot_duplications, plot_genes_in_ogs, plot_species_specific_ogs.

Usage

plot_orthofinder_stats(tree = NULL, stats_list = NULL, xlim = c(0, 1))

Arguments

tree	Tree object as returned by treeio::read.*, a family of functions in the treeio package to import tree files in multiple formats, such as Newick, Phylip, NEXUS, and others. If your species tree was inferred with Orthofinder (using STAG), the tree file is located in Species_Tree/SpeciesTree_rooted_node_labels.txt. Then, it can be imported with treeio::read_tree(path_to_file).
stats_list	(optional) A list of data frames with Orthofinder summary stats as returned by the function read_orthofinder_stats. If this list is given as input, nodes will be labeled with the number of duplications.
xlim	Numeric vector of x-axis limits. This is useful if your node tip labels are not visible due to margin issues. Default: c(0, 1).

Value

A panel of ggplot objects.

Examples

data(tree)
dir <- system.file("extdata", package = "cogeqc")
stats_list <- read_orthofinder_stats(dir)
plot_orthofinder_stats(tree, xlim = c(0, 1.5), stats_list = stats_list)

almeidasilvaf/cogeqc documentation built on Jan. 29, 2024, 7:20 a.m.