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!

-----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

-----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