visualizepairfeat {SeqFeatR}

Visualize pairs of sequence alignment positions associated with sequence feature.

Description

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

Usage

visualizepairfeat(path_to_file_assocpairfeat_csv_result = NULL, save_name_pdf, 
    significance_level = 0.01)

Arguments

path_to_file_assocpairfeat_csv_result

csv file with results from SeqFeatRs assocpairfeat 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

For every feature (if only one p-value is below given threshold ('significance_level')) an output page (pdf page) 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.

Note

Only use files generated from SeqFeatRs assocpairfeat function.

Author(s)

Bettina Budeus

See Also

assocpairfeat

Examples

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

#Usage
visualizepairfeat(
	path_to_file_assocpairfeat_csv_result=assocpairfeat_result,
	save_name_pdf="vispairfeat_plot.pdf", 
	significance_level=0.05)