ct_boxplot_ng Version 2.0
Sep 7, 2000
by Darrin Stewart and Michael Zuker
Documentation for ct_boxplot_ng
Files
ct_boxplot_setcolor.inc
ct_boxplot.col
copyright_ps.inc
copyright_img.inc
ct_boxplot_ng.c
ct_boxplot_read_ct.inc
ct_boxplot_ng.doc
ct_boxplot.h
ct_boxplot_general.inc
ct_boxplot_ps.inc
ct_boxplot_img.inc
Makefile_ct_ng
Sets the colors
List of colors to use
Displays the copyright message the ps output
Displays the copyright message for the png/jpg
Main source code (non-interactive)
Reads the ct files
This file
General .h file
General functions
Generates postscript output
Generates png/jpg output
Makefile for ct_boxplot_ng
This program reads multiple ct files and displays them. It can create
png,jpg or postscript output.
When zooming, if the dots are large enough,
the program displays a dot in multiple colors to indicate which
structure produces overlap at this point.
If the dots are too small for this, the dot is displayed as gray
for partial overlap, or black for full overlap.
The lower triangle uses black or gray for
overlap. Which structure, if any, for the lower display can be chosen
with the -a switch.
When the output switches
from multiple colors to black and gray for showing overlap depends
on the dot size. It depends on how many pixels or points are available
for each color based on the dot size. Alter STRIPE_PS,STRIPE_GIF,
in ct_boxplot.h to change when this happens.
ct_boxplot.col is read at execution time and can be edited for
user preference.
This file is searched for in 1. The present working directory,
2. The directory specified by environmental
variable "MFOLDLIB"
3. The directory dat within the directory
specified by the environmental variable
"MFOLD"
______________________________________________________________________
Each ct file must contain only one structure.
It must start as:
741 ENERGY =
1 G
2 G
3 C
-238.3
0
2
1
3
2
4
mok-lacZ + gtgtaa
618
1
617
2
616
3
The first line must contain the information shown.
The number of bases, energy and name are each taken from it.
The = is required too.
The number of bases is compared to the number in the file.
The first entry on each line after the first must indicate which base
is specified. The program will exit if there are any skips or duplicates.
They must start at 1.
The program warns against The second entry, the base, being different
within different CT files.
All ct files on a given run must be the same length.
________________________________________________________________________
Sample usage:
ct_boxplot_ng name1.ct name2.ct name3.ct
The program accepts 1 to 200 ct files.
The files are display in 15 colors. Files 15 throught 200
use the same color.
Valid arguments:
-a Structure
Display This structure in the lower striangle,
where the value for Structure corresponds to the nth ct
file in the command line.
Value -3 is Partial and Full overlap (Default)
-2 is none.
-1 is Full overlap only.
0 is Partial overlap only.
-10 for 3 sequences, display partial overlap using
color for content.
-b
Enable clear
background
-d direct/
Look for ct files in directory direct, end with /
-f
Force gray to be shown in multicolor.
-j
Draw postscript dots at least 1/72 inch=1 point in size.
-jpg
Creates jpg.
This requires tgd_jpg.
-l i j
image
Label the point i,j in the png,jpg or zoomed postscript
-m value
Magnify dot size by value. (.2 to 100.)
-o name_out
Specify name of output file as
name_out.ps or name_out.png or name_put.jpg
-pg
Create both png and postscript output or
both jpg and postscript output.
Specify -png or -jpg to determine which is produced.
-png
Creates png.
This requires tgd_png.
-r Res
Specify png/jpg resolution from 30 to 300
-s
Save the tgd file for editing the png or jpg
-t "TITLE"
Use TITLE as a title rather than the first line of the
first ct file. (Quotes are required.)
-w
Create .gifdat for web zooming
(Obscure Option) This option creates a file name.gifdat that
contains
resolution,left,top,step_x,step_y,farthest_base,display_l,display_t
for zooming on gif images being displayed on the WEB.
left is location of left border of image.
top is location of top border of image.
step_x is pixels per basepair dot horizontally.
step_y is pixels per basepair dot vertically.
farthest base is the label on the top right corner.
display_l is leftmost value on displayed horizontal axis
display_t is smallest value on displayed vertical axis
-y s rowi colj
-z l r t b
Zoom with scale s about row i column j
s can be from .1 to 200
specify a zoom region: left,right,top,bottom bases.
The postscript output is now easy to alter to adjust the colors,
or the size of dots. In particular, it is possible to make
dots of a particular structure largerto emphasize it. If enlarged,
it will show up under its partial overlap dots.
For many structures, it is possible to change the color for
a particular sequence to see it. While the program uses the
same for color for structures beyond 15, a particular color can
be set here to make a higher numbered structure appear in a different
color. In fact, for 50 structures all 50 can be set to different colors.
The postscript output contains counts for each type of dot. For 3
sequences,
if they are interpreted for content, the count is for the upper triangle
when it is turned on there with -i.
If it is displayed in the lower triangle only with -a -10,
then the count applies there.
Most counts only count dots in the upper triangle.
Counts for individual sequences count the dots shown in that color as
well as those of the sequence used for partial or full overlap.