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ggplot simple question.

3 messages · rmje, John Kane, Jeff Newmiller

rmje
# 
I have a matrix like this

Name                                   1                            2                                
3                                 4                            5 
NM_001039514	1.033557047	0.7469879518	0.9004524887	0.8613861386	0.7952499048
NM_001039723	1.0759493671	1.2315789474	0.8666666667	1.1142857143
0.9428011471
NM_001042605	0.9897435897	0.8870431894	1.1038062284	0.7407407407	0.744530664
NM_001048207	1.0070422535	0.9319727891	0.9015151515	0.8296438884
0.7290217712

I want to plot each row in a single graph and then use multiplot to put them
all together in a single graph.
How do you plot the rows?


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John Kane
# 
That does not look like a matrix but a data frame.  Do a class(dataname) to check.

It is much better to present the data in a useable format.  Have a look at ?dput for a way to provide the data.

However if we assulme your data is xx, this may do what you want if I understand you correcctly.

xx1  <-data.frame( t(xx[, 2:6]))
xx1[,5]  <- names(xx[2:6])
names(xx1)  <- c(letters[1:4], "Name")
ggplot(xx1, aes(x=factor(Name), a))  + geom_point()

John Kane
Kingston ON Canada
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Jeff Newmiller
#
On Sat, 12 May 2012, rmje wrote:

            

      
      
      
    

        
Please use dput() to generate R commands to recreate your sample data.
For example, I type "dta <- " and then copy-paste the output of dput(dta):

dta <- structure(list(Name = structure(1:4, .Label = c("NM_001039514",
"NM_001039723", "NM_001042605", "NM_001048207"), class = "factor"),
     X1 = c(1.033557047, 1.0759493671, 0.9897435897, 1.0070422535
     ), X2 = c(0.7469879518, 1.2315789474, 0.8870431894, 0.9319727891
     ), X3 = c(0.9004524887, 0.8666666667, 1.1038062284, 0.9015151515
     ), X4 = c(0.8613861386, 1.1142857143, 0.7407407407, 0.8296438884
     ), X5 = c(0.7952499048, 0.9428011471, 0.744530664, 0.7290217712
     )), .Names = c("Name", "X1", "X2", "X3", "X4", "X5"), class = 
"data.frame", row.names = c(NA,
-4L))

You have stated that this is a matrix, but it obviously contains text for 
row names.  The standard output of write.table doesn't put a heading above 
row names, so this looks more like a data frame. I don't know how your row 
names were set up as numerics... when I used read.table() to pull your 
example in, the headings were changed to valid data frame column names by 
prepending "X".  Your use of dput() would have made all thes questions 
irrelevant.

AFAIK all plotting in R assumes data series are vectors or columns, not 
rows, so some data structure transformation is needed before your 
desired plots can be generated.

There is probably more than one way to skin this cat, but here is one way:

library(reshape2)
library(ggplot2)
dtalong <- melt( dta, "Name" )
dtalong$x <- as.numeric( substring( as.character( dtalong$variable ), 2 ) )
ggplot( dtalong, aes( x=x, y=value ) ) +
   geom_point() +
   facet_wrap( ~Name, ncol=1 )

If you are not familiar with melt, use ?melt to read the help and 
experiment with it, and use the str() function to study dta and dtalong 
to see how the data are moved around.

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