On 6/20/2011 11:25 AM, Vickie S wrote:
Hi Dennis,
It looks like something is wrong about configuration of ggplot dependency with
plyr.Since i saw some threads about this particular error message.
I tried several times by installing different versions of plyr but it did not
work.
========
sampledata= matrix(c(1.002, 1.76, 0.67, 0.99, 1.38, 1.0, 0.5, 0.78, 1.003,0.57, 0.99, 0.58, 0.76, 1.23, 1.45, .78,1.43, 1.34, 1.0, 0.9), ncol = 5, dimnames =
list(c("cond1", "cond2","cond3", "cond4"), c("col1","col2", "col3", "col4",
"col5")))
sdata<- melt(sampledata) # melt method for matrices
sdata$grp<- factor(c('grp1', 'grp1', 'grp2', 'grp3'))
sdata$time<- rep(1:5, each = 4)
library(ggplot2)
h<- ggplot(sdata, aes(time, value))
h + geom_point(aes(colour = cond), size = 2.5) + geom_line(aes(colour = cond),
size = 1)
Error in get("make_aesthetics", env = x, inherits = TRUE)(x, ...) :
could not find function "empty"
sessionInfo()
R version 2.10.1 (2009-12-14)
x86_64-apple-darwin9.8.0
locale:
[1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] grid stats graphics grDevices utils datasets methods base
other attached packages:
[1] plyr_1.1 ggplot2_0.8.9 proto_0.3-8 reshape_0.8.3
loaded via a namespace (and not attached):
[1] tools_2.10.1
Any suggestions ?
This works for me:
library("reshape")
library("ggplot2")
# note that the dimnames are now a named list, the names
# of which become the column names when melted.
sampledata <- matrix(c(1.002, 1.76, 0.67, 0.99, 1.38,
1.0, 0.5, 0.78, 1.003,0.57, 0.99, 0.58, 0.76,
1.23, 1.45, .78,1.43, 1.34, 1.0, 0.9),
ncol = 5,
dimnames = list(cond=c("cond1", "cond2","cond3", "cond4"),
time = c("col1","col2", "col3", "col4", "col5")))
sdata <- melt(sampledata) # melt method for matrices
# This works without error
ggplot(sdata, aes(time, value)) +
geom_point(aes(colour = cond), size = 2.5) +
geom_line(aes(colour = cond), size = 1)
# This might be what you meant, though. By default, the group
# aesthetic is an interaction of all the categorical variables
# (here, time and cond) and a separate thing (point or line) is
# drawn for each group. So there is only one point along each
# line (which doesn't make for much of a line). Override this to
# make one line per cond.
ggplot(sdata, aes(time, value, colour=cond)) +
geom_point(size = 2.5) +
geom_line(aes(group = cond), size = 1)
> sessionInfo()
R version 2.13.0 (2011-04-13)
Platform: x86_64-pc-mingw32/x64 (64-bit)
locale:
[1] LC_COLLATE=English_United States.1252
[2] LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages:
[1] grid stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] ggplot2_0.8.9 proto_0.3-9.2 reshape_0.8.4 plyr_1.5.2
loaded via a namespace (and not attached):
[1] digest_0.5.0
In particular, the most recent version of plyr is 1.5.2; I assume it
would work with R 2.10.1, but I don't know. You may need to install it
as a source package.
Vickie S
----------------------------------------
Date: Mon, 20 Jun 2011 07:28:12 -0700
Subject: Re: [R] profile plot in R
From: djmu...@gmail.com
To: is...@live.com
CC: jwiley.ps...@gmail.com; r-help@r-project.org
Hi:
Typically a profile plot is a plot over time for each of n subjects
(aka a 'spaghetti plot'). Here's a revision of your code to yield a
profile plot in ggplot2, although it's not clear for what the grouping
variable is meant.
sampledata= matrix(c(1.002, 1.76, 0.67, 0.99, 1.38, 1.0, 0.5, 0.78,
1.003,0.57, 0.99, 0.58, 0.76, 1.23,
1.45, .78,
1.43, 1.34, 1.0, 0.9), ncol = 5,
dimnames = list(c("cond1", "cond2",
"cond3", "cond4"),
c("col1",
"col2", "col3", "col4", "col5")))
sdata<- melt(sampledata) # melt method for matrices
sdata$grp<- factor(c('grp1', 'grp1', 'grp2', 'grp3'))
sdata$time<- rep(1:5, each = 4)
library(ggplot2)
h<- ggplot(sdata, aes(time, value))
h + geom_point(aes(colour = cond), size = 2.5) +
geom_line(aes(colour = cond), size = 1)
Hope this is enough to get you started...
Dennis
On Mon, Jun 20, 2011 at 5:20 AM, Vickie S<is...@live.com> wrote:
Hi thanks for the help.
Here is the error message i got. I could not figure out what goes wrong here.
======
require(ggplots2)
sampledata=data.frame(c(1.002, 1.76, 0.67, 0.99), c(1.38,1.0,0.5, 0.78),
c(1.003,0.57,0.99, 0.58),c(0.76,1.23, 1.45, .78), c(1.43, 1.34, 1.0, 0.9))
rownames(sampledata)=c("cond1", "cond2", "cond3", "cond4")
colnames(sampledata)=c("col1", "col2", "col3", "col4", "col5")
grp=c("grp1", "grp1", "grp2", "grp3")
sampledata=cbind(sampledata, grp)
long.dat=melt(sampledata[,1:5], idvars=as.character(rownames(sampledata)),
measure.vars=as.character(colnames(sampledata)[1:5]), variable_name="cols")
ggplot(long.dat, aes(x = cols, y = value)) +
+ geom_line(aes(colour = sampledata$grp)) +
+ facet_grid(~ rownames(sampledata))
Error in get("make_aesthetics", env = x, inherits = TRUE)(x, ...) :
could not find function "empty"
=====
thanks again,
Vickie S
----------------------------------------
CC: r-help@r-project.org
From: jwiley.ps...@gmail.com
Subject: Re: [R] profile plot in R
Date: Sat, 18 Jun 2011 08:24:01 -0700
To: is...@live.com
Hi,
Another easy option would be to convert your data to "long" format and then use
ggplot2 or lattice. Something like (though not exact without a reproducible example):
require(ggplot2)
long.dat<- melt(your_data, arguments)
ggplot(long.dat, aes(x = variable, y = value)) +
geom_line(aes(colour = group)) +
facet_grid(~ condition)
HTH,
Josh
On Jun 17, 2011, at 12:43, Vickie S<is...@live.com> wrote:
Hi friends,
I have a matrix with following format.
group var1 var2 .......varN
c1 group1 1.2399 1.4990....-1.4829
c2 group4 0.8989 0.7849.....1.8933
...
...
c100 group10 .....
I want to draw a profile plot
of each condition c1 to c100, which rows in above matrix and each line
representing a row should be uniquely colored according to the group(1
to 10).
I think this is simple task but I could not figure out how to set the colors.
Any help would be appreciated.
thanks
-Vickie
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______________________________________________
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
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Senior Research Associate, Department of Surgery
Oregon Health & Science University
______________________________________________
R-help@r-project.org mailing list
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
