R help - Nov 2014 - How to use ggplot2

Dear All!!
I'll try to plot a barplot using aggplot2

head(alt)
  as.factor.data...7..    Col ColMat  Fastq  miseq
1                  189    158    158    158    104
2                  190  54272  54272  54272  32122
3                  191 301574 301574 301574 152625
4                  192 161620 161620 161620 100469
5                  193  61263  61263  61263  38109
6                  194  83800  83800  83800  40095
> 
p<- ggplot(data = alt, aes(y = alt[,2]))  +  geom_bar() 

Error : Mapping a variable to y and also using stat="bin".
  With stat="bin", it will attempt to set the y value to the count of
cases in each group.
  This can result in unexpected behavior and will not be allowed in a future
version of ggplot2.
  If you want y to represent counts of cases, use stat="bin" and
don't map a variable to y.
  If you want y to represent values in the data, use stat="identity".
  See ?geom_bar for examples. (Defunct; last used in version 0.9.2)
How can resolve this problem?
My data are in column: each columns are conditions and each row rappresnt a
sample
thanks for your help!
M


	[[alternative HTML version deleted]]

It is useful to have a reproducable example
https://github.com/hadley/devtools/wiki/Reproducibility
 http://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible-example

However is this somethingl like what you want?  Note I changed variable names
and removed caps to make life easier and renamed the dataset to dat1 (just
handier for me).  I think "col" as a reserved word should not be used.
It seemed to be causing a problem.

library(ggplot2)
dat1  <-  structure(list(aa = 189:194, bb = c(158L, 54272L, 301574L, 161620L,
61263L, 83800L), colmat = c(158L, 54272L, 301574L, 161620L, 61263L, 
83800L), fastq = c(158L, 54272L, 301574L, 161620L, 61263L, 83800L
), miseq = c(104L, 32122L, 152625L, 100469L, 38109L, 40095L)), .Names =
c("aa",
"bb", "colmat", "fastq", "miseq"), class
= "data.frame", row.names = c(NA,
-6L))

p1  <-  ggplot(dat1, aes( as.factor(aa), y = bb, fill = as.factor(aa))) 
p1  <-  p1 + geom_bar(stat = "identity")
p1 


John Kane
Kingston ON Canada

> -----Original Message-----
> From: jarod_v6 at libero.it
> Sent: Wed, 26 Nov 2014 18:04:21 +0100 (CET)
> To: r-help at r-project.org
> Subject: [R] How to use ggplot2
> 
> Dear All!!
> I'll try to plot a barplot using aggplot2
> 
> head(alt)
>   as.factor.data...7..    Col ColMat  Fastq  miseq
> 1                  189    158    158    158    104
> 2                  190  54272  54272  54272  32122
> 3                  191 301574 301574 301574 152625
> 4                  192 161620 161620 161620 100469
> 5                  193  61263  61263  61263  38109
> 6                  194  83800  83800  83800  40095
>> 
> p<- ggplot(data = alt, aes(y = alt[,2]))  +  geom_bar()
> 
> Error : Mapping a variable to y and also using stat="bin".
>   With stat="bin", it will attempt to set the y value to the
count of
> cases in each group.
>   This can result in unexpected behavior and will not be allowed in a
> future version of ggplot2.
>   If you want y to represent counts of cases, use stat="bin" and
don't
> map a variable to y.
>   If you want y to represent values in the data, use
stat="identity".
>   See ?geom_bar for examples. (Defunct; last used in version 0.9.2)
> How can resolve this problem?
> My data are in column: each columns are conditions and each row rappresnt
> a sample
> thanks for your help!
> M
> 
> 
> 	[[alternative HTML version deleted]]
> 
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> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
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