heatmap2

How to download and try this example

Usage: pl -gif [-map] heatmap2.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"


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

// group into bins 4 cM wide..
filter:
   ##set A = $numgroup( @@2, 4, mid )
   @@1 @@A

// set up the plotting area
#proc areadef
rectangle: 1 1 6 3
areacolor: white
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: color
details: gray(0)
label: >20
tag: 21

#proc legendentry
sampletype: color
details: gray(0.3)
label: 11-20
tag: 11 
  
#proc legendentry
sampletype: color
details: gray(0.5)
label: 6 - 10
tag: 6

#proc legendentry
sampletype: color
details: gray(0.8)
label: 1 - 5
tag: 1

#proc legendentry
sampletype: color
details: gray(1)
label: 0
tag: 0
 

// use proc scatterplot to count # of instances and pick appropriate color from legend..
#proc scatterplot
yfield: chr
xfield: cM
cluster: yes
dupsleg: yes
rectangle: 4 1 
  

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