plot_all_stages: Plot the Expression of One Orthogroup in Both Species

In othomantegazza/crossr: Functions For Cross Species Quantitative Transcriptomics

Plot the Expression of One Orthogroup in Both Species

Description

plot_all_stages is a wrapper for stripchart and plots a stripchart and a line plot of the expression of an orthogroup across all samples

Usage

plot_all_stages(orthogroup, ogset, species, condition, main = "",
  use_annos = FALSE, annos_col = NULL, ...)

Arguments

orthogroup	a character string
ogset	an ogset class element
species	a string used to encode the species info in the design formula
condition	a string used to encode the experimental conditions of the samples in the columns of the dset
main	the title of the plot
use_annos	logical; if TRUE, functional annotation from og_annos will be displayed in the plot subtitle. Defaults to FALSE
annos_col	a character string with the name of the column of og_annos that contains the functional annotation that should be displayed. Defaults to NULL. It must be provided if use_annos is set to TRUE.
...	arguments to be passed to stripchart

Details

This function takes an orthogroup ID and an ogset class element as arguments. It plots a stripchart of the expression of all the stages; The title of the stripchart contains details on: how many genes are in the orthogroup, the cluster that contain the ogroup (if any), the F-value for the interaction term.

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