Re: [R] to represent color range on plot segment
Dear Jim, Thank you very much for your code. There is no problem with df[df[,2]>0,3]<-color.scale(df[df[,2]>0,2],c(1,0),1,c(0,1)) but the other has an error message if there is a negative value, like > df[df[,2]<0,3]<-color.scale(df[df[,2]<0,2],1,c(1,0),c(1,0)) Error in rgb(reds, greens, blues) : color intensity -0.157746, not in [0,1] Kindly update me with your comments. Regards, karthick -- View this message in context: http://r.789695.n4.nabble.com/to-represent-color-range-on-plot-segment-tp3773392p3775990.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] to represent color range on plot segment
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 __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] to represent color range on plot segment
?colorRamp On Sat, Aug 27, 2011 at 2:07 PM, 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 > > Thanks in advance, > regards, > karthick > > > > -- > View this message in context: > http://r.789695.n4.nabble.com/to-represent-color-range-on-plot-segment-tp3773392p3773392.html > Sent from the R help mailing list archive at Nabble.com. > > __ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. > -- Jim Holtman Data Munger Guru What is the problem that you are trying to solve? __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] to represent color range on plot segment
On Sat, Aug 27, 2011 at 11:07 AM, karthicklakshman wrote: > Dear R community, > > With an advantage of being "NEW" to R, I would like to post a very basic > query here, Really? I found two posts with your name on it dating from October and November of 2010. http://r-project.markmail.org/search/?q=karthicklakshman > > 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) Please read the posting guide, linked at the bottom of this mail, especially the part about 'reproducible example'. You provided the data, but no code to show that you made a serious effort to solve this problem on your own. Moreover, since this is related to gene expression data, the Bioconductor list may be more appropriate for future questions re gene expression: http://www.bioconductor.org/help/mailing-list/ although this one is within the purview of R-help IMO. Use the sign of value (?sign) as an indicator variable to which you can map colors. I'd also think about creating a value for location (midpoint, maybe?) to simplify the plot call. It shouldn't be too difficult to do this in any of base graphics, lattice or ggplot2. Dennis > > 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 > > Thanks in advance, > regards, > karthick > > > > -- > View this message in context: > http://r.789695.n4.nabble.com/to-represent-color-range-on-plot-segment-tp3773392p3773392.html > Sent from the R help mailing list archive at Nabble.com. > > __ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. > __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
