visualizepair {SeqFeatR}

Visualize pairs of alignment positions that jointly mutate

Description

Creates a pdf output with a visualization of the results from the analysis from SeqFeatRs assocpair function.

Usage

visualizepair(path_to_file_assocpair_csv_result = NULL, 
    save_name_pdf, significance_level = 0.01)

Arguments

path_to_file_assocpair_csv_result

csv file with results from SeqFeatRs assocpair function. For reference see example file.

save_name_pdf

name of file to which results are saved in pdf format.

significance_level

significance value below which the results of the analysis are considered to be relevant enough to be plotted.

Details

An output is created with a sequence position versus sequence position graphic. Every dot color(one position with the other position) is based on its p-value. The color code is on the right side. In contrast to visualizepairfeat, no feature information will be used.

Note

Only use files generated from SeqFeatRs assocpair function.

Author(s)

Bettina Budeus

See Also

assocpair

Examples

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

#Usage
visualizepair(
	path_to_file_assocpair_csv_result=assocpair_result,
	save_name_pdf="vispair_plot.pdf",
	significance_level=0.05)