Re: ecdf function and privacy issue
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adam.l...@pnc.com
Mar 11, 2013, 4:44:22 PM3/11/13
to Sarita Paranjpe, ggplot2
Hi,
I don't have an answer to your question, but I did want to point out that ggplot2 recently added stat_ecdf, which allows you to get cumulative distributions on the fly that obey grouping and faceting.
Adam Loveland
Folks :
I am trying to plot a graph to show cumulative frequency distribution of three data sets of unequal length. The shortest data set (dark brown) isn't as smooth as the rest (see the plot attached). Why so ?
My code :
c = read.delim("xtev_v3.3beta_newtranscript_Vv.fa._codonbias_LLRfiltered_lessthan_orf100_331_filtered.txt", header=T, sep="\t")
f = read.delim("noncoding_GL172663_SIZE2000.fa._codonbias.txt", header=T, sep="\t")
e = read.delim("xtropMRNA_processed.fa._codonbias.txt", header=T, sep="\t")
c1 = as.matrix(c[,4])
f1 = as.matrix(f[,2])
e1 = as.matrix(e[,2])
cbind.fill<-function(...){
nm <- list(...)
nm<-lapply(nm, as.matrix)
n <- max(sapply(nm, nrow))
do.call(cbind, lapply(nm, function (x)
rbind(x, matrix(, n-nrow(x), ncol(x)))))
}
bound = cbind.fill(c1,f1,e1)
y = data.frame(bound)
z = melt(y)
z = ddply(z, .(variable), transform, ecd = ecdf(value)(value))
d = ggplot(z, aes(x = value, y = ecd)) + geom_line(aes(group = variable, colour = variable), size = 1.5) + xlim(c(0,10))
d + scale_color_manual(values = c("#993404", "#984EA3", "#FF7F00"))
ggsave("331_filtered_ecdf.pdf")
Privacy :
Sometimes i have sent confidential data set as dput to the group so solve a particular problem. I was okay with it until i figured that people can look up my mails sent to ggplot2 by simply googling for my name. Can we solve this ? Or do i have have to change my personal settings ? Please help.
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I don't have an answer to your question, but I did want to point out that ggplot2 recently added stat_ecdf, which allows you to get cumulative distributions on the fly that obey grouping and faceting.
Adam Loveland
| From: | Sarita Paranjpe <heys...@gmail.com> |
| To: | ggplot2 <ggp...@googlegroups.com> |
| Date: | 03/11/2013 12:05 PM |
| Subject: | ecdf function and privacy issue |
| Sent by: | ggp...@googlegroups.com |
Folks :
I am trying to plot a graph to show cumulative frequency distribution of three data sets of unequal length. The shortest data set (dark brown) isn't as smooth as the rest (see the plot attached). Why so ?
My code :
c = read.delim("xtev_v3.3beta_newtranscript_Vv.fa._codonbias_LLRfiltered_lessthan_orf100_331_filtered.txt", header=T, sep="\t")
f = read.delim("noncoding_GL172663_SIZE2000.fa._codonbias.txt", header=T, sep="\t")
e = read.delim("xtropMRNA_processed.fa._codonbias.txt", header=T, sep="\t")
c1 = as.matrix(c[,4])
f1 = as.matrix(f[,2])
e1 = as.matrix(e[,2])
cbind.fill<-function(...){
nm <- list(...)
nm<-lapply(nm, as.matrix)
n <- max(sapply(nm, nrow))
do.call(cbind, lapply(nm, function (x)
rbind(x, matrix(, n-nrow(x), ncol(x)))))
}
bound = cbind.fill(c1,f1,e1)
y = data.frame(bound)
z = melt(y)
z = ddply(z, .(variable), transform, ecd = ecdf(value)(value))
d = ggplot(z, aes(x = value, y = ecd)) + geom_line(aes(group = variable, colour = variable), size = 1.5) + xlim(c(0,10))
d + scale_color_manual(values = c("#993404", "#984EA3", "#FF7F00"))
ggsave("331_filtered_ecdf.pdf")
Privacy :
Sometimes i have sent confidential data set as dput to the group so solve a particular problem. I was okay with it until i figured that people can look up my mails sent to ggplot2 by simply googling for my name. Can we solve this ? Or do i have have to change my personal settings ? Please help.
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[attachment "331_filtered_ecdf.pdf" deleted by Adam Loveland/FinAdmin/CLE/PNC]
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