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Last data update: 2014.03.03

R: Visualize odds ratios and p-values from SeqFeatRs assocpoint

orPlot

R Documentation

Visualize odds ratios and p-values from SeqFeatRs assocpoint

Description

Creates odds ratio/p-value plots for every feature and sequence alignment position.

Usage

orPlot(path_to_file_assocpoint_results = NULL,
	save_name_pdf, separator = ";",
	number_of_cases = 2, odds_column_position = c(6),
	p_value_column_position = c(2), name_column_position = c(2), freq = 7,
	sequence_column_position = NULL, max_y_axis = 50, interval = 10,
        has_color = 0, bias = 5, p_or_od = "P")

Arguments

`path_to_file_assocpoint_results`	csv file with results from SeqFeatRs assocpoint function. For reference see example file.
`save_name_pdf`	name of file to which results are saved in csv format.
`separator`	letter with which csv is separated (usually ";" or ",", or "\t").
`number_of_cases`	number of different features in input file.
`odds_column_position`	column number of first odds ratios.
`p_value_column_position`	column number of first p-value.
`name_column_position`	column number of feature name in first row.
`freq`	frequency of repeat in columns with more than two cases.
`sequence_column_position`	column number of first amino acid/nucleotide sequence.
`max_y_axis`	estimated guess of the best p-value/ highest Odds ratio. Usuall the number behind the e as positive number.
`interval`	interval on the y axis.
`has_color`	if there should be presented another kind of information as a color feature. See details.
`bias`	bias of colors. Select with integer values if you want the first color further down. See details.
`p_or_od`	if p-values or OR should be plotted as height. "P" for p-value, "OR" for Odds ratios.

Details

Creates from SeqFeatRs assocpoint results a graphical output where each position in the sequence alignment is shown as bar. The height of this bar can be the log10 of p-value at this position or the odds ratio, the direction information (up or down) based upon odds ratio (below one is down, above one is up). If the user adds a column number for an amino acid or DNA base, this sequence is added above each bar.

The bar plot can be additionally colored by another type of information (e.g. display p-values as height, odds ratio as direction and sequence entropy as color). The source of this color information has to be added in 'has_color' as a column number. This column can be added manually before creating this plot. The column should contain only numbers between zero and one. A bias can be given to change the color distribution (see R-function colorRampPalette).

Author(s)

Bettina Budeus

Examples

#Input file
assocpoint_result <- system.file("extdata", "assocpoint_results.csv", package="SeqFeatR")
	
#Usage
orPlot(
	path_to_file_assocpoint_results=assocpoint_result, 
	save_name_pdf="orPlot.pdf",
	separator=";",
	number_of_cases=8,
	odds_column_position=6,
	p_value_column_position=2,
	name_column_position=2,
	freq=7,
	sequence_column_position=NULL,
	max_y_axis=4,
	interval=0.2,
	has_color=0,
	bias=5,
	p_or_od="P")

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