[R] qplot: plotting precipitation data

[Rui Barradas]

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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