[R] qplot: plotting precipitation data

Hadley Wickham hadley at rice.edu
Thu Sep 20 14:19:03 CEST 2012 

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 <ruipbarradas at 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: ruipbarradas at sapo.pt
>>> Sent: Sun, 16 Sep 2012 13:13:47 +0100
>>> To: jrkrideau at 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: hnorpois at googlemail.com
>>>>> Sent: Sat, 15 Sep 2012 18:39:54 +0200
>>>>> To: r-help at 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]]
>>>>>
>>>>> ______________________________________________
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>
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