CODEWITHSUNDEEP
rggplot2
aindap
aindap

Reputation: 71

adding geom_text to ggfluctuation

Hi I am writing an R function to generate a fluctuation plot using ggplot2

fluctuation <- function(filename)
    x=read.table(filename,sep=",")

    mydata=melt(x)$value
    mydata=matrix(mydata,ncol=4, byrow=T)
    colnames(mydata) <-c("AA", "AB", "BB","no.call")
    rownames(mydata) <-c("AA", "AB", "BB", "no.call")

    data.melt=melt(mydata)

    names(data.melt)<-c("pgm", "truth", "value")

    p <- ggfluctuation(data.melt)+ xlab("Truth") + ylab("Pgmsnp") 

    p2 <- p  + geom_text(aes(label=data.melt$value),colour="black", main="whole-exome capture")


    return (p2)

When I run this code:

fluctuation("file.csv")

I get the following error:

Error in eval(expr, envir, enclos) : object 'data.melt' not found

However, if I return p, its fine. So there is some issue with

geom_text(aes(label=data.melt$value),colour="black", main="whole-exome capture")

But I can't figure it out. I'm still a bit of a ggplot2 newbie. I googled around and found similar questions, but I can't seem to fix my instance. Can someone help point me in the right direction?

Upvotes: 1

Views: 209

Answers (2)

aindap
aindap

Reputation: 71

Well, there is something I don't understand about how R handles functions. If I explicitly glob all my input files and then make the plots by iterating through the list of file inputs I want to make a plot for, it works. 

library("ggplot2")
library("reshape2")



files <- dir(getwd(), pattern = "*.csv", full.names = FALSE)

for (i in 1:length(files)) {

    x=read.table(files[i],sep=",")
    mydata=melt(x)$value
    mydata=matrix(mydata,ncol=4, byrow=T)
    colnames(mydata) <-c("AA", "AB", "BB","no.call")
    rownames(mydata) <-c("AA", "AB", "BB", "no.call")

    data.melt=melt(mydata)

    names(data.melt)<-c("pgm", "truth", "value")
    plotname <- paste(files[i], "png", sep=".")
    p <- ggfluctuation(data.melt) + geom_text(aes(label=data.melt$value)) +xlab("Truth") + ylab("Pgmsnp") + theme(axis.text.x= element_text(size=rel(1.5))) + theme(axis.text.y= element_text(size=rel(1.5))) + theme(axis.title.x = element_text(size = rel(1.5))) + theme(axis.title.y= element_text(size = rel(1.5))) +  opts(title = files[i]) + theme(plot.title = element_text(size = rel(.95)))
    ggsave(p, file=plotname)



}

Upvotes: 0

JoFrhwld
JoFrhwld

Reputation: 9037

I'm not so familiar with the operation of `ggfluctuation(), but if it's similar to other ggplot functions, you should change it to

p <- ggfluctuation(data.melt)+ xlab("Truth") + ylab("Pgmsnp") 
p2 <- p  + geom_text(aes(label=value),colour="black", main="whole-exome capture")

ggplot layers inherit the data frame from the original ggplot(), or in this case, ggfluctuation() layer. aes() looks to the data frame it's inheriting when it maps variables, so in this case, only use aes(label=value).

Upvotes: 1

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