tartan {SeqFeatR}

Visualize association of mutation pairs and features from two (comparable) analyses.

Description

Combines the results of two of SeqFeatRs assocpair or assoctuple analyses in one plot.

Usage

tartan(path_to_file_assocpair_csv_result=NULL,
 path_to_file_assocpair_csv_result2=NULL, save_name_pdf, space,
 colors, name_positions, names, ticks, first_position_1,
 second_position_1, value_1, first_position_2, second_position_2,
 value_2, with_distance_matrix, path_to_distance_matrix)

Arguments

path_to_file_assocpair_csv_result

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

path_to_file_assocpair_csv_result2

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

save_name_pdf

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

space

space between blocks. See details.

colors

the colors of the tartan plot. See details.

name_positions

Positions on x and y axis where the labels should be inserted.

names

labels to be inserted on x and y axis. Beware! name_position and names must have the same length!

ticks

ticks which should mark interesting spots and are also the breakpoints on which the blocks are separated. See details.

first_position_1

column in which first alignment position is located in the first csv file.

second_position_1

column in which second alignment position is located in the first csv file.

value_1

column in which value to be shown is located in first csv file.

first_position_2

column in which first alignment position is located in the second csv file.

second_position_2

column in which second alignment position is located in the second csv file.

value_2

column in which value to be shown is located in csv second file.

with_distance_matrix

if there is a distance matrix available and should be used.

path_to_distance_matrix

path to the distance matrix. Can be zero or empty.

Details

For each sequence x sequence position for one feature the corresponding (p-)values are added as a colored dot.

The input files may be the results from SeqFeatRs assocpair or assoctuple analyses, but any csv file with two different columns of sequence positions and one column with values is sufficient. The values should be in a comparable range, but they can be other information as p-values (e.g. mutual or direct information or distance matrix given as an extra input file).

The displayed colors are chosen by the user. The format for 'colors' must be color names in quotes (e.g. "red", "blue", etc.) separated by "," (without the double quotes). More colors will give a better distinction.

To distinguish different parts of the sequence (e.g proteins, markers, etc.) the user may add sequence positions as ticks ('ticks') at which the graphical display is split and a little space ('space') is inserted. The user can also add names to be displayed on the x-axis/y-axis ('name_positions', 'names').

Author(s)

Bettina Budeus

See Also

assocpair, assoctuple

Examples

#Input files
assocpair_result <- system.file(
                    "extdata", "shared_mutations_result_for_tartan.csv", package="SeqFeatR")
assocpair_result2 <- system.file(
                    "extdata", "assocpair_results.csv", package="SeqFeatR")

#Usage
tartan(
	path_to_file_assocpair_csv_result=assocpair_result,
	path_to_file_assocpair_csv_result2=assocpair_result2,
	save_name_pdf="tartan_plot.pdf",
	space=5,
	colors=c("wheat", "darkblue", "black", "green"),
	name_positions=c(1,30),
	names=c("S","F"),
	ticks=c(10,30),
	first_position_1=2,
	second_position_1=3,
	value_1=4,
	first_position_2=2,
	second_position_2=3,
	value_2=11,
	with_distance_matrix=FALSE,
	path_to_distance_matrix=NULL)