SeqFeatR (version 0.3.3)

smallmanhattan: A small version of manhattan plot

Description

Creates a small version of the manhattan plot from assocpoint with annotated alignment positions.

Usage

smallmanhattan(path_to_file_csv, save_name_png, save_name_svg, feature,
       corrected=FALSE, x_axis_breaks)

Value

A small version of the manhattan plot as png/svg picture file. svg files can be changed more easily than png files.

Arguments

path_to_file_csv

csv file with results from assocpoint. For reference see example file.

save_name_png

name of file to which graphic is saved in png format.

save_name_svg

name of file to which graphic is saved in svg format.

feature

column number in input csv file with the values. See details.

corrected

if the corrected p-values should be used.

x_axis_breaks

x axis breaks to be displayed. See details.

Author

Bettina Budeus

Details

The input file should be a result file from SeqFeatRs assocpoint.

The feature, that should be displayed as an extra manhattan plot, must be given just like it is displayed in the csv file, e.g for HLA-A2, insert "A2" as value for feature. If you want to show the corrected p-values, change corrected to TRUE.

The x_axis_breaks will mark ticks on the x axis, so that a special alignment position can be displayed. Those axis breaks have to be given in the following format only:
- starting an ending with quotes
- between those quotes comma separated ascending alignemnt position numbers (pleas keep in mind, that the plot will only display a little more than the highest alignment number, whatever big number you have given here)
- no blanks
- can be left empty (""), then breaks with 50 positions will be displayed

See Also

assocpoint

Examples

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

#Usage
smallmanhattan(
	assocpoint_result,
        save_name_png = "small_manhattan.png", 
        save_name_svg = "small_manhattan.svg", 
        feature = "A2",
        corrected = FALSE, 
        x_axis_breaks = "1,10,16,20,30,40")
}