On Fri, Dec 4, 2009 at 11:53 AM, Sunny Srivastava <research.b...@gmail.com> wrote: > Dear R-Helpers, > I am not very experienced in using lattice and I am still in the learning > stage > > I have a data set which looks like this: (I have deleted a few lines in > order to save space) > > Chromosome marker Marker.Name Distance > 1 1 1 PeMm261 0.0000 > 2 1 2 Xtxp8 10.1013 > .. > 20 1 20 EbMi148 210.3099 > 21 1 21 Xtxp25 232.0118 > 22 2 1 EcMm152 0.0000 > 23 2 2 EeMp342 5.1474 > ... > 36 2 15 EaMp217 124.5115 > 37 2 16 EaMp131 136.9033 > .... > 40 3 1 TEak2908 0.0000 > 41 3 2 Xtxp303 4.7094 > 42 3 3 EhMm195 10.1694 > > (I have 11 chromosome in total .. so conditioning on chromosome gives me 11 > panels) > > This is a data.frame which contains Chromosome Number, Marker Number for > that chromosome and the corresponding Marker.Name and Distance. > > I want to plot the genetic distance conditioned on chromosome and the marker > name listed below the distance where the marker is situated on chromosome > (something like this picture) > > Panel 1 : Chromosome 1 > > |-------------------|------------------------- (so and so forth) > PeMm261 Xtxp8 > <---- 10.1013 -> (the distance b/w these markers is same as the > corresponding value in marker$Distance - see 1 and 2 row in the sample > output) > > and similarly for other chromosomes.
Here's one attempt; hopefully it will give you useful ideas: df <- structure(list(Chromosome = c(1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 3L, 3L, 3L), marker = c(1L, 2L, 20L, 21L, 1L, 2L, 15L, 16L, 1L, 2L, 3L), Marker.Name = structure(c(7L, 11L, 3L, 9L, 4L, 5L, 2L, 1L, 8L, 10L, 6L), .Label = c("EaMp131", "EaMp217", "EbMi148", "EcMm152", "EeMp342", "EhMm195", "PeMm261", "TEak2908", "Xtxp25", "Xtxp303", "Xtxp8"), class = "factor"), Distance = c(0, 10.1013, 210.3099, 232.0118, 0, 5.1474, 124.5115, 136.9033, 0, 4.7094, 10.1694)), .Names = c("Chromosome", "marker", "Marker.Name", "Distance"), class = "data.frame", row.names = c("1", "2", "20", "21", "22", "23", "36", "37", "40", "41", "42")) library(lattice) ## single panel dotplot(Chromosome ~ Distance, df, mnames = df$Marker.Name, panel = function(x, y, ..., mnames, subscripts) { panel.dotplot(x, y, ...) panel.text(x, y, labels = mnames[subscripts], srt = 90, adj = -0.1) }) ## multiple panels dotplot( ~ Distance | factor(Chromosome), df, mnames = df$Marker.Name, layout = c(1, 3), strip = FALSE, strip.left = TRUE, panel = function(x, y, ..., mnames, subscripts) { panel.dotplot(x, y, ...) panel.text(x, y, labels = mnames[subscripts], srt = 90, adj = -0.1) }) -Deepayan > > > I tried: > > plt1 = dotplot( ~ Distance | Chromosome, data=marker,par.strip.text = > list(cex = 0.75), layout = c(1,11), > lattice.options=list(legend="right"), xlab="Distance in cM", > ylab="", > scales= list(cex=0.5), > > panel = function(x, y) { > panel.grid(h=1,v= 345) > panel.xyplot(x, y,pch=20,type="o",lwd="2",cex=1.5) > }, > ) > > update(plt1, main="Genetic Map", > strip = strip.custom(factor.levels = c("1", > "2","3","4","5","6","7","8","9","10","11"), strip.levels = TRUE)) > > > This gives me the location of markers on the respective chromosomes > corresponding to the distances in the above data.frame. The markers are just > shown as points. > > > MY QUESTIONS - 1) If I want to label these dots with the corresponding > marker names - How do I do that? > 2) Is there a way in lattice - to know which > panel I am in. > > I tried inserting panel.text in the panel function - but it doesn't like > that. (I also played around with scales - but without any success) > > Any help will be greatly appreciated. > > Thx, > S. > > ------------------------------------------------------------------------------- >> sessionInfo() > R version 2.9.1 (2009-06-26) > i386-pc-mingw32 > > locale: > LC_COLLATE=English_United States.1252;LC_CTYPE=English_United > States.1252;LC_MONETARY=English_United > States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] lattice_0.17-25 qtl_1.14-2 > > loaded via a namespace (and not attached): > [1] grid_2.9.1 tools_2.9.1 > > [[alternative HTML version deleted]] > > ______________________________________________ > 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.