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Last data update: 2014.03.03

R: Create volcano plot

volcanoplot

R Documentation

Create volcano plot

Description

Creates a pdf output file with a volcano plot out of the results from SeqFeatRs assocpoint.

Usage

volcanoplot(path_to_file_assocpoint_csv_result,
 save_name_pdf, p_values_pos, odds_pos, pos_pos,
 level_of_sig_p, level_of_sig_odds)

Arguments

`path_to_file_assocpoint_csv_result`	csv file with results from SeqFeatRs assocpoint. For reference see example file.
`save_name_pdf`	name of file to which results are saved in pdf format.
`p_values_pos`	column number with p-values.
`odds_pos`	column number with odds ratios.
`pos_pos`	column number with positions.
`level_of_sig_p`	level of significance p values.
`level_of_sig_odds`	level of significance odds ratios.

Details

Plots log$_10$ Odds ratios versus -log$_10$ p-values and annotates the dots with sequence positions.

Author(s)

Bettina Budeus

Examples

#Input file
assocpoint_result <- system.file("extdata", "assocpoint_results.csv", package="SeqFeatR")

#Usage
volcanoplot(
	path_to_file_assocpoint_csv_result=assocpoint_result,
	save_name_pdf="volcano_plot.pdf",
	p_values_pos = 3,
	odds_pos = 6,
	pos_pos = 1,
	level_of_sig_p = 0.05,
	level_of_sig_odds = 1)

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(SeqFeatR)
Error in library(SeqFeatR) : there is no package called 'SeqFeatR'
Execution halted