orPlot: 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.

Author

Bettina Budeus

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).

Examples

Run this code

#Input file
if (FALSE) {
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")
}