ggplot_all_stages: Plot the Expression of One Orthogroup in Both Species with...

In othomantegazza/crossr: Functions For Cross Species Quantitative Transcriptomics

Plot the Expression of One Orthogroup in Both Species with ggplot2

Description

ggplot_all_stages is a wrapper for ggplot2 that plots a stripchart and a line plot of the expression of an orthogroup in both species.

Usage

ggplot_all_stages(orthogroups, ogset, species_var, condition_var,
  colours = c("darkblue", "#56B4E9"), use_annos = FALSE)

Arguments

orthogroups	a character vector with the orthogroups for the plot
ogset	an ogset class element
species_var	a character string with the name of column of coldata that encodes for the species from which the samples originates.
condition_var	a character string with the name of column of coldata that encodes the experimental conditions under which you are comparing the samples
colours	a character vector with the colours for the plot
use_annos	logical; if TRUE the functional annotation from og_annos will be displayed in the plot subtitle. Defaults to FALSE

Details

This function takes one (ot many) orthogroup IDs and an ogset class element as arguments. It plots a stripchart of the expression of all the stages.

You can also provided a vector of multiple orthogroup IDs, ggplot_all_stages will plot all of them using faceting.

The function returns a ggplot object that can be further customized with all basic ggplot2 functionalities.

othomantegazza/crossr documentation built on Feb. 1, 2023, 7:44 a.m.