snpmap1

How to download and try this example

Usage: pl -gif snpmap1.htm
Uses data file snpmap.dat .
For brevity, only chromosomes 1-7 and X are represented in this example.



// set demo defaults..
#setifnotgiven SLIST = "@9,@11"
#setifnotgiven CGI = "http://ploticus.sourceforge.net/cgi-bin/showcgiargs"


// SLIST is a comma-delimited list of field numbers (eg @4) indicating strain(s) of interest
//       (the integers correspond to field positions in the SNP map data file).

// read in the SNP map data file..
#proc getdata
file: snpmap.dat
fieldnameheader: yes
#if @SLIST != ""
  // if we are concentrating on strain(s) of interest, run some processing to flag
  // entries where strain(s) of interest are all present, and to flag entries where
  // strains of interest have different alleles..
  // showresults: yes
  filter:
     // see if alleles of interest are all present, and if there are differences
     ##set LIST = $expand( "@SLIST" )
     ##set ALLPRESENT = 0
     ##set DIFF = 0
     ##if = !in @@LIST
       ##set ALLPRESENT = 1
     ##endif
     ##if $homogeneous( @@LIST ) = 0
       ##set DIFF = 1
     ##endif
     @@1 @@2 @@ALLPRESENT @@DIFF 
#endif

// 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.stubslide: 0.08
// yaxis.stubreverse: yes
yaxis.label: chromosome
yaxis.axisline: no
yaxis.tics: no
yaxis.grid: color=gray(0.9)
yaxis.clickmap: xygrid

xrange: -3 120
xaxis.label: position (cM)
xaxis.grid: color=gray(0.9) width=0.4 style=1 dashscale=3
xaxis.axisline: no
xaxis.tics: no
xaxis.clickmap: xygrid
xaxis.stubs: inc 10
xaxis.stubrange: 0
xaxis.stubdetails: adjust=0,0.15

// do 2nd x axis across top
#proc xaxis
location: max
axisline: no
tics: no
stubs: inc 10
stubdetails: adjust=0,0.2 size=6
stubformat: %3.0f cM
stubrange: 0


#if @SLIST = ""
  #set ALLCOLOR = teal
#else
  #set ALLCOLOR = gray(0.8)
#endif
 
// use proc scatterplot to cluster duplicates upward, effectively creating little bars..
#proc scatterplot
yfield: chr
xfield: cM
symbol: shape=square radius=0.01 fillcolor=@ALLCOLOR style=filled
cluster: yes
clustermethod: upward
clusterfact: 0.4

#saveas A

#if @SLIST != ""
  // overlay little black bars counting entries where all strains of interest are present..
  #proc scatterplot
  #clone A
  select: @@3 = 1
  symbol: shape=square radius=0.01 fillcolor=black style=filled

  // overlay little red bars counting entries where strains of interest have different alleles..
  #proc scatterplot
  #clone A
  select: @@3 = 1 && @@4 = 1 
  symbol: shape=square radius=0.01 fillcolor=red style=filled
  
#endif
  
// do legend if appropriate..
#if @SLIST != ""
  #set N = $count( "*", @SLIST )
  #if @N = 1
    #proc legendentry
    sampletype: color
    details: black
    label: involving strain(s)
  
    #proc legendentry
    sampletype: color
    details: @ALLCOLOR
    label: not involving strain(s)
  
  #elseif @N > 1
    #proc legendentry
    sampletype: color
    details: red
    label: selected strains differ
  
    #proc legendentry
    sampletype: color
    details: black
    label: selected strains alike
  
    #proc legendentry
    sampletype: color
    details: @ALLCOLOR
    label: other SNPs 
  
  #endif
  
  #proc legend
  location: max-1.3 min+0.8
  textdetails: size=6
  swatchsize: 0.075

#endif

// draw scale bracket..
#proc line
linedetails: width=0.4
points:  100(s) 5(s) 100(s) 4(s) 
	 100(s) 5(s) 99(s) 5(s) 
	 100(s) 4(s) 99(s) 4(s)

#proc annotate
location: 102(s) 5(s)
textdetails: align=L size=7 adjust=0,0.05
text: = 25 SNPs