colorgrid2

How to download and try this example

Usage: pl -gif [-map] colorgrid2.htm

This color grid involves processing raw data by 
counting occurances within ranges, then mapping counts to colors by range.

Uses data file snpmap.dat .
For brevity, only chromosomes 1-7 and X are represented in this example.



#set SYM = "radius=0.08 shape=square style=filled"
#setifnotgiven CGI = "http://ploticus.sourceforge.net/cgi-bin/showcgiargs"

#proc page
backgroundcolor: black
color: white

// read in the SNP map data file..
#proc getdata
file: snpmap.dat
fieldnameheader: yes

// group into bins 10 cM wide..
filter:
   ##set A = $numgroup( @@2, 10, mid )
   @@1 @@A


// set up the plotting area
#proc areadef
rectangle: 1 1 6 3
yscaletype: categories
clickmapurl: @CGI?chrom=@@YVAL&cM=@@XVAL
ycategories: 
	1
	2
	3
	4
	5
	6
	7
	X
	
yaxis.stubs: usecategories
yaxis.stubdetails: adjust=0.2,0
//yaxis.stubslide: 0.08
yaxis.label: chromosome
yaxis.axisline: no
yaxis.tics: no
yaxis.clickmap: xygrid

xrange: -3 120
xaxis.label: position (cM)
xaxis.axisline: no
xaxis.tics: no
xaxis.clickmap: xygrid
xaxis.stubs: inc 10
xaxis.stubrange: 0
xaxis.stubdetails: adjust=0,0.15


// set up legend for color gradients..
#proc legendentry
sampletype: symbol
details: fillcolor=yellow @SYM
label: >40
tag: 41

#proc legendentry
sampletype: symbol
details: fillcolor=orange @SYM
label: 31-40
tag: 31
  
#proc legendentry
sampletype: symbol
details: fillcolor=red @SYM
label: 21-30
tag: 21

#proc legendentry
sampletype: symbol
details: fillcolor=lightpurple @SYM
label: 11-20
tag: 11

#proc legendentry
sampletype: symbol
details: fillcolor=blue @SYM
label: 1 - 10
tag: 1
 

// use proc scatterplot to count # of instances and pick appropriate color from legend..
#proc scatterplot
yfield: chr
xfield: cM
cluster: yes
dupsleg: yes
  

// display legend..
#proc legend
location: max-0.7 min+0.8
textdetails: size=6