proteinortho_curves

This script creates accumulation curves for pan- and core-genomes calculated with Proteinortho (Lechner et al. 2011.)

Requirements

• R
• R package "ggplot2"
• R package "grid"
• R package "optparse"
• Proteinortho output calculated with "-singles" option

Versions I used when writing the script:
- proteinortho v5.16b
- R version 3.6.3
- ggplot2_3.3.5
- optparse_1.6.6

Usage

proteinortho_curves.r [options]

Calculations and first plot

Proteinortho must have been run using the "-singles" option!

proteinortho_curves.r -p <your_project_name>.proteinortho -i <number_of_iterations> 
-o <output_prefix> [plot parameters]

Output:

<output_prefix>_proteinortho_curves.txt
<output_prefix>_proteinortho_curves.png

-i parameter:

In each iteration the script randomly permutates the columns (strains) of the proteinortho output. It then adds the strains in the new order of the columns to the Core- and Pan-genome calculations. The number of iterations is usually 100 and it should not be lower than 10.

Plotting existing calculations

As the calculations can take quite some time, depending on the number of iterations, this is the way to redraw the plot for an existing proteinortho_curves table and experiment with the plot parameters.

proteinortho_curves.r -d TRUE -t <output_prefix>_proteinortho_curves.txt 
-o <output_prefix> [plot parameters]

Output:

<output_prefix>_proteinortho_curves.png

If you don't want Pan- and Core-Genome size text on the plot, set --x_pan_text and --y_pan_text to a higher number (above 2) and the text should not be visible

Options/Plot Parameters Overview

Options:
	-p PROTEINORTHO, --proteinortho=PROTEINORTHO
		Output from proteinortho <myproject.proteinortho>

	-i ITERATIONS, --iterations=ITERATIONS
		Number of iterations to perform [default=10]

	-d DRAW_ONLY, --draw_only=DRAW_ONLY
		Draw plot from a previously calculated table [default=FALSE]

	-t TABLE, --table=TABLE
		When -d TRUE, previously calculated output from proteinortho_curves.r <proteinortho_curves.txt>

	-o OUTPUT, --output=OUTPUT
		Name of output file(s) [default=proteinortho_curves]

	--plot_width=PLOT_WIDTH
		Width of the plot [default=10]

	--plot_height=PLOT_HEIGHT
		Height of the plot [default=7]

	--pan_color=PAN_COLOR
		Color of the pan-genome boxplots [default=#82c6b8]

	--pan_text_color=PAN_TEXT_COLOR
		Color of the pan-genome text [default=#0d9a7e]

	--core_color=CORE_COLOR
		Color of the core-genome boxplots [default=#c35b8e]

	--core_text_color=CORE_TEXT_COLOR
		Color of the pan-genome text [default=#8b104e]

	--plot_title=PLOT_TITLE
		Title of the plot [default=Proteinortho Pan- and Core-Genome Size]

	--plot_title_size=PLOT_TITLE_SIZE
		Size of the title of the plot [default=12]

	--x_axis_title=X_AXIS_TITLE
		Title of the x axis [default=Number of genomes]

	--y_axis_title=Y_AXIS_TITLE
		Title of the y axis [default=Number of orthologs]

	--axis_title_size=AXIS_TITLE_SIZE
		Size of the x and y axis titles [default=10]

	--axis_text_size=AXIS_TEXT_SIZE
		Size of the x and y axis text [default=8]

	--axis_text_mode=AXIS_TEXT_MODE
		How many tick marks to show on x axis. 1=all, 2=every second, etc [default=1]

	--x_pan_text=X_PAN_TEXT
		Relative x position of the pan-genome text [default=0.84]

	--y_pan_text=Y_PAN_TEXT
		Relative y position of the pan-genome text [default=0.5]

	--x_core_text=X_CORE_TEXT
		Relative x position of the core-genome text [default=0.84]

	--y_core_text=Y_CORE_TEXT
		Relative y position of the core-genome text [default=0.46]

	--pan_core_text_size=PAN_CORE_TEXT_SIZE
		Relative size of the pan- and core-genome text [default=1]

	-h, --help
		Show this help message and exit