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').
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(SeqFeatR)
Error in library(SeqFeatR) : there is no package called 'SeqFeatR'
Execution halted