It was a bit hard for me to follow the thread and figure out exactly what the problem is that you're having, but I think it has something to do with the ticks on the x axis not appearing in the correct order?
It's probably related to this issue: https://github.com/hadley/ggplot2/issues/577 I believe it's happening because the x scale gets "trained" separately on xmin and xmax values, and if that happens when one of them _doesn't_ have all the factor levels, the factor levels get recomputed, and are placed in lexicographical order. One workaround is to use scale_x_discrete(drop=FALSE). -Winston mydata <- structure(list(chrom = structure(c(3L, 3L, 3L, 3L, 3L, 3L), .Label = c("chr1", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", "chr17", "chr18", "chr19", "chr2", "chr3", "chr4", "chr5", "chr6", "chr7", "chr8", "chr9", "chrX"), class = "factor"), start = c(5291000L, 10988025L, 11767950L, 11840900L, 12267450L, 12276675L), end = c(5291926L, 10988526L, 11768676L, 11841851L, 12268076L, 12277051L), peak = c(8L, 7L, 8L, 8L, 12L, 7L)), .Names = c("chrom", "start", "end", "peak" ), row.names = c(NA, -6L), class = "data.frame") # Continuous x axis - rects are very, very narrow, but they're there ggplot(mydata) + geom_rect(aes(xmin = start, xmax = end, ymin = 0, ymax = peak)) # Continuous x axis and geom_bar: Width of each bar is determined by # resolution of the data. Still narrow, but not as much. ggplot(mydata) + geom_bar(aes(x = start, y = peak), stat="identity") unique(mydata$start) unique(mydata$end) # Convert start and end to factors with the same set of levels levels <- sort(unique(c(mydata$start, mydata$end))) mydata$start <- factor(mydata$start, levels = levels) mydata$end <- factor(mydata$end, levels = levels) # X ticks appear in wrong order ggplot(mydata) + geom_rect(aes(xmin = start, xmax = end, ymin = 0, ymax = peak)) # Can specify the limits directly ggplot(mydata) + geom_rect(aes(xmin = start, xmax = end, ymin = 0, ymax = peak)) + xlim(as.character(levels)) # Or can use scale_x_discrete(drop = FALSE) ggplot(mydata) + geom_rect(aes(xmin = start, xmax = end, ymin = 0, ymax = peak)) + scale_x_discrete(drop = FALSE) On Thu, Sep 20, 2012 at 7:19 AM, Hadley Wickham <had...@rice.edu> wrote: > Hmmm, I'm not sure what the problem is, but I suspect it's related to > the fact the xmin and xmax have different factors levels and there are > some bugs in ggplot2 related to combining factors in some situations > (it's basically impossible to always do it right). > > Explicitly ensuring the levels were the same doesn't help, but setting > the xlims does. Winston, is this related to some of the other bugs > we've been working on lately? > > mydata <- structure(list(chrom = structure(c(3L, 3L, 3L, 3L, 3L, 3L), .Label = > c("chr1", "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", > "chr17", "chr18", "chr19", "chr2", "chr3", "chr4", "chr5", "chr6", "chr7", > "chr8", "chr9", "chrX"), class = "factor"), start = c(5291000L, 10988025L, > 11767950L, 11840900L, 12267450L, 12276675L), end = c(5291926L, 10988526L, > 11768676L, 11841851L, 12268076L, 12277051L), peak = c(8L, 7L, 8L, 8L, 12L, > 7L)), > .Names = c("chrom", "start", "end", "peak" ), row.names = c(NA, -6L), class = > "data.frame") > > ggplot(mydata) + > geom_rect(aes(xmin = start, xmax = end, ymin = 0, ymax = peak)) > > unique(mydata$start) > unique(mydata$end) > > levels <- sort(unique(c(mydata$start, mydata$end))) > mydata$start <- factor(mydata$start, levels = levels) > mydata$end <- factor(mydata$end, levels = levels) > > ggplot(mydata, aes(x = start)) + > geom_rect(aes(xmin = start, xmax = end, ymin = 0, ymax = peak)) + > xlim(as.character(levels)) > > > On Sun, Sep 16, 2012 at 11:11 AM, Rui Barradas <ruipbarra...@sapo.pt> wrote: >> Maybe a bug in ggplot2::geom_rect? >> >> I'm Cceing this to Hadley Wickham, maybe he has an answer. >> >> Rui Barradas >> >> Em 16-09-2012 17:04, John Kane escreveu: >>>> >>>> -----Original Message----- >>>> From: ruipbarra...@sapo.pt >>>> Sent: Sun, 16 Sep 2012 13:13:47 +0100 >>>> To: jrkrid...@inbox.com >>>> Subject: Re: [R] qplot: plotting precipitation data >>>> >>>> Hello, >>>> >>>> Relative to the op's "request" for rectangls, I'm not understanding them. >>> >>> Neither am I really, I just googled a couple of sites for possible >>> "chromatin precipitation" graphs and since the OP was not sure of the name >>> of the geom made the assumption that they wanted a bar chart as it seemed >>> like the simplest graph matching the 'rectanngles" statement. I was >>> assuming a terminology or language problem here and I could not see any >>> reason the OP wanted purely rectangles. >>> >>>> In your plot using geom_bar, the levels of as.factor(start) are sorted >>>> ascending. If both >>>> >>>> > as.factor(mydata$start) >>>> [1] 5291000 10988025 11767950 11840900 12267450 12276675 >>>> Levels: 5291000 10988025 11767950 11840900 12267450 12276675 >>>> > as.factor(mydata$end) >>>> [1] 5291926 10988526 11768676 11841851 12268076 12277051 >>>> Levels: 5291926 10988526 11768676 11841851 12268076 12277051 >>>> >>>> also are, why isn't geom_rect ploting them by that order? >>>> >>>> p2 <- ggplot(mydata, aes(x = as.factor(start), y = peak)) >>>> p2 + geom_rect(aes(xmin = as.factor(start), xmax = as.factor(end), ymin >>>> = 0, ymax = peak)) >>>> >>>> The level 5291926 is place last. Shouldn't it be expected to plot as >>>> first? >>> >>> This is far beyond my knowledge of ggplot but I would certainly think it >>> should. >>> as.numeric( as.factor(mydata$start))) >>> [1] 1 2 3 4 5 6 >>> >>> so why would we get something like 2 3 4 5 6 1 if I am reading this >>> correctly? >>> >>> >>>> Rui Barradas >>>> >>>> Em 16-09-2012 00:20, John Kane escreveu: >>>>> >>>>> Thanks for the data. It makes things much easier. >>>>> >>>>> Do you want a bar chart (i.e. geom = bar in qplot or geom_bar in >>>>> ggplot)? That sounds like what you mean when you speak of rectangles. >>>>> >>>>> If so try this ggplot) command -- I almost never use qplot() so I am not >>>>> quite sure how to specify it there. >>>>> >>>>> p <- ggplot(mydata , aes(as.factor(start), peak )) + geom_bar(stat= >>>>> "identity", ) >>>>> p >>>>> >>>>> >>>>> John Kane >>>>> Kingston ON Canada >>>>> >>>>> >>>>>> -----Original Message----- >>>>>> From: hnorp...@googlemail.com >>>>>> Sent: Sat, 15 Sep 2012 18:39:54 +0200 >>>>>> To: r-help@r-project.org >>>>>> Subject: [R] qplot: plotting precipitation data >>>>>> >>>>>> Dear list, >>>>>> >>>>>> I wish to plot chromatin precipitation data: I would like to have a >>>>>> rectangles (x:end-start, y:peak) but I do not have an idea how to >>>>>> define >>>>>> x >>>>>> (in terms of qplot syntax) and to choose the correct geom. >>>>>> mydata is a subset of a larger file. >>>>>> >>>>>>> mydata >>>>>> >>>>>> chrom start end peak >>>>>> 1 chr11 5291000 5291926 8 >>>>>> 2 chr11 10988025 10988526 7 >>>>>> 3 chr11 11767950 11768676 8 >>>>>> 4 chr11 11840900 11841851 8 >>>>>> 5 chr11 12267450 12268076 12 >>>>>> 6 chr11 12276675 12277051 7 >>>>>>> >>>>>>> dput(mydata) >>>>>> >>>>>> structure(list(chrom = structure(c(3L, 3L, 3L, 3L, 3L, 3L), .Label = >>>>>> c("chr1", >>>>>> "chr10", "chr11", "chr12", "chr13", "chr14", "chr15", "chr16", >>>>>> "chr17", "chr18", "chr19", "chr2", "chr3", "chr4", "chr5", "chr6", >>>>>> "chr7", "chr8", "chr9", "chrX"), class = "factor"), start = c(5291000L, >>>>>> 10988025L, 11767950L, 11840900L, 12267450L, 12276675L), end = >>>>>> c(5291926L, >>>>>> 10988526L, 11768676L, 11841851L, 12268076L, 12277051L), peak = c(8L, >>>>>> 7L, 8L, 8L, 12L, 7L)), .Names = c("chrom", "start", "end", "peak" >>>>>> ), row.names = c(NA, -6L), class = "data.frame") >>>>>> Thanks for some instructions. >>>>>> >>>>>> Hermann Norpois >>>>>> >>>>>> [[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. >>>>> >>>>> ____________________________________________________________ >>>>> FREE 3D EARTH SCREENSAVER - Watch the Earth right on your desktop! >>>>> >>>>> ______________________________________________ >>>>> 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. >>> >>> ____________________________________________________________ >>> FREE 3D MARINE AQUARIUM SCREENSAVER - Watch dolphins, sharks & orcas on >>> your desktop! >>> Check it out at http://www.inbox.com/marineaquarium >>> >>> >> >> ______________________________________________ >> 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. > > > > -- > RStudio / Rice University > http://had.co.nz/ ______________________________________________ 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.
