[R] making a barplot with table of experimental conditions underneath (preferably ggplot2)

[John Kane]

Oops, that last line  of code should read
df.plot + scale_x_discrete( labels = df$labs)

John Kane
Kingston ON Canada


> -----Original Message-----
> From: jrkrideau at inbox.com
> Sent: Thu, 14 Nov 2013 09:02:19 -0800
> To: n.hubner at ncmls.ru.nl, r-help at r-project.org
> Subject: RE: [R] making a barplot with table of experimental conditions
> underneath (preferably ggplot2)
> 
> Hi Nina,
> I think the following code does what you want (thanks to Jim Lemon for
> showing me what you wanted in terms of x-axis tick labels)
> 
> However I  think that barcharts are generally evil  so I changed your
> geom_bar to geom_point.  Feel free to change it back if your discipline
> requires it but I think it shows your data better
> 
> Also you were doing some unnecessary extraction of dat from the
> data.frame so I just included a "data =" statement in qplot and changed
> the variable names in it to the original df names. This makes for cleaner
> and more readable code.
> 
> df <- data.frame (experiment=c("E1","E2","E3","E4"), mean = c(3,4,5,6),
> stdev=c(0.1,0.1,0.05,0.2), method = c("STD","STD", "FP", "FP"), enzyme =c
> ("T","T/L","T","T/L"), denaturation=c("U","U","0.05%RG", "0.1%RG"))
> 
> df$labs  <-  paste(df[,4],"\n ",df[,5], "\n ",df[,6]) # create labels
> 
> df.plot <- qplot(experiment,mean,data = df, xlab="", ylab="# peptides
> identified")+
>   geom_point(fill="grey")+
>   geom_errorbar(aes(x=experiment, ymin=mean-stdev, ymax=mean+stdev),
> width=0.25)
> 
> p + scale_x_discrete( labels = df$labs)
> 
> I hop
> John Kane
> Kingston ON Canada
> 
> 
>> -----Original Message-----
>> From: n.hubner at ncmls.ru.nl
>> Sent: Wed, 13 Nov 2013 14:24:28 +0000
>> To: r-help at r-project.org
>> Subject: [R] making a barplot with table of experimental conditions
>> underneath (preferably ggplot2)
>> 
>> Dear all,
>> 
>> my data looks the following:
>> 
>> df <- data.frame (experiment=c("E1","E2","E3","E4"), mean = c(3,4,5,6),
>> stdev=c(0.1,0.1,0.05,0.2), method = c("STD","STD", "FP", "FP"), enzyme
>> =c
>> ("T","T/L","T","T/L"), denaturation=c("U","U","0.05%RG", "0.1%RG"))
> 
>> I would like to make a bar plot with standard deviation which I solved
>> the following way:
>> 
>> x <- df$experiment
>> y <- df$mean
>> sd <- df$stdev
>> 
>> df.plot <- qplot(x,y,xlab="", ylab="# peptides identified")+
>>   geom_bar(colour="black", fill="darkgrey")+
>>   geom_errorbar(aes(x=x, ymin=y-sd, ymax=y+sd), width=0.25)
>> 
>> df.plot
>> 
> 
>> However, as the labels for the x-axis (the bars) I do not want the
>> experiment number, as now, but instead a table containing the other
>> columns of my data.frame (method, enzyme, denaturation) with the
>> description in the front and the certain 'value' below the bars.
>> 
>> I am looking forward to your suggestions!
>> 
>> With best wishes,
>> 
>> Nina
>> ______________________________________________
>> 
>> Dr. Nina C. Hubner
>> scientist quantitative proteomics
>> 
>> Dep. of Molecular Biology, Radboud University Nijmegen, The Netherlands
>> e-mail: n.hubner at ncmls.ru.nl
>> tel: +31-24-3613655
>> 
>> Visiting address:
>> NCMLS, Dept of Molecular Biology (route 274)
>> Geert Grooteplein 26/28
>> 6525 GA Nijmegen
>> The Netherlands
>> 
>> 
>> 
>> 
>> The Radboud University Medical Centre is listed in the Commercial
>> Register of the Chamber of Commerce under file number 41055629.
>> 
>> 
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>> 
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> 
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