[R] qplot: plotting precipitation data

[John Kane]

> -----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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