On 08/28/2011 04:07 AM, karthicklakshman wrote:
Dear R community,
With an advantage of being "NEW" to R, I would like to post a very basic
query here,
I am in need of representing gene expression data which ranges from -0.09 to
+4, on plot "segment". please find below the data df, the expression values
are in df[,2]. kindly help me with the code, so that I can represent the
values with a clear color gradient (something like -0.09 to 0 as red
gradient and 0 to +4 as green gradient)
location value
15 chr+:14001-15001 0.99749499
16 chr+:15001-16001 0.99957360
17 chr+:16001-17001 0.99166481
18 chr+:17001-18001 0.97384763
19 chr+:18001-19001 0.94630009
20 chr+:19001-20001 0.90929743
21 chr+:20001-21001 0.86320937
22 chr+:21001-22001 0.80849640
23 chr+:22001-23001 0.74570521
24 chr+:23001-24001 0.67546318
25 chr+:24001-25001 0.59847214
26 chr+:25001-26001 0.51550137
27 chr+:26001-27001 0.42737988
28 chr+:27001-28001 0.33498815
29 chr+:28001-29001 0.23924933
30 chr+:29001-30001 0.14112001
31 chr+:30001-31001 0.04158066
32 chr+:31001-32001 -0.05837414
33 chr+:32001-33001 -0.15774569
34 chr+:33001-34001 -0.25554110
35 chr+:34001-35001 -0.35078323
36 chr+:35001-36001 -0.44252044
37 chr+:36001-37001 -0.52983614
38 chr+:37001-38001 -0.61185789
39 chr+:38001-39001 -0.68776616
40 chr+:39001-40001 -0.75680250
41 chr+:40001-41001 -0.81827711
42 chr+:41001-42001 -0.87157577
43 chr+:42001-43001 -0.91616594
44 chr+:43001-44001 -0.95160207
Hi karthick,
Here's one way to do it:
library(plotrix)
df[,3]<-NA
df[df[,2]<0,3]<-color.scale(df[df[,2]<0,2],1,c(0,1),c(0,1))
df[df[,2]>0,3]<-color.scale(df[df[,2]>0,2],c(1,0),1,c(0,1))
df[,3] will then be a vector of colors that range from red at the
minimum value to white at 0 to green at the maximum value.
Jim
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