R help - Apr 2016 - Removing NAs from dataframe (for use in Vioplot)

Hi

First post and a relative R newbie....

I am using the vioplot library to produce some violin plots. I have an input CSV
with columns off irregular length that contain NAs. I want to strip the NAs out
and produce a multiple violin plot automatically labelled using the headers. At
the moment I do this

Code:?
ds1 = read.csv("http://www.lecturematerials.co.uk/data/spelling.csv")
library(vioplot)
y6<-na.omit(ds1$y6)
y5<-na.omit(ds1$y5)
y4<-na.omit(ds1$y4)
y3<-na.omit(ds1$y3)
y2<-na.omit(ds1$y2)
y1<-na.omit(ds1$y1)
vioplot(y6, y5, y4,y3,y2,y1,horizontal=TRUE, names=c("Y6",
"Y5","Y4","Y3","Y2","Y1"), col
= "lightblue")


Two queries:

1. Is there a more elegant way of automatically stripping the NAs, passing the
columns to the function along with the header names??

2. Can I easily add the sample size to each violin plotted??

thanks

mike
						


---
Mike Smith

> On Apr 30, 2016, at 12:58 PM, Mike Smith <mike at hsm.org.uk> wrote:
> 
> Hi
> 
> First post and a relative R newbie....
> 
> I am using the vioplot library to produce some violin plots. I have an
input CSV with columns off irregular length that contain NAs. I want to strip
the NAs out and produce a multiple violin plot automatically labelled using the
headers. At the moment I do this
> 
> Code: 
> ds1 =
read.csv("http://www.lecturematerials.co.uk/data/spelling.csv")
> library(vioplot)
> y6<-na.omit(ds1$y6)
> y5<-na.omit(ds1$y5)
> y4<-na.omit(ds1$y4)
> y3<-na.omit(ds1$y3)
> y2<-na.omit(ds1$y2)
> y1<-na.omit(ds1$y1)
> vioplot(y6, y5, y4,y3,y2,y1,horizontal=TRUE, names=c("Y6",
"Y5","Y4","Y3","Y2","Y1"), col
= "lightblue")
> 
> 
> Two queries:
> 
> 1. Is there a more elegant way of automatically stripping the NAs, passing
the columns to the function along with the header names??
> 
ds2 <- lapply( ds1, na.omit)

> 2. Can I easily add the sample size to each violin plotted??
> ?violplot
No documentation for ?violplot? in specified packages and libraries:
you could try ???violplot?
> 
> thanks
> 
> mike
> 						
> 
> 
> ---
> Mike Smith
> 
> ______________________________________________
> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
David Winsemius
Alameda, CA, USA

> On Apr 30, 2016, at 4:16 PM, David Winsemius <dwinsemius at
comcast.net> wrote:
> 
> 
>> On Apr 30, 2016, at 12:58 PM, Mike Smith <mike at hsm.org.uk>
wrote:
>> 
>> Hi
>> 
>> First post and a relative R newbie....
>> 
>> I am using the vioplot library to produce some violin plots.
It's a package,  .... not a library.
>> I have an input CSV with columns off irregular length that contain NAs.
I want to strip the NAs out and produce a multiple violin plot automatically
labelled using the headers. At the moment I do this
>> 
>> Code: 
>> ds1 =
read.csv("http://www.lecturematerials.co.uk/data/spelling.csv")
>> library(vioplot)
>> y6<-na.omit(ds1$y6)
>> y5<-na.omit(ds1$y5)
>> y4<-na.omit(ds1$y4)
>> y3<-na.omit(ds1$y3)
>> y2<-na.omit(ds1$y2)
>> y1<-na.omit(ds1$y1)
>> vioplot(y6, y5, y4,y3,y2,y1,horizontal=TRUE, names=c("Y6",
"Y5","Y4","Y3","Y2","Y1"), col
= "lightblue")
>> 
>> 
>> Two queries:
>> 
>> 1. Is there a more elegant way of automatically stripping the NAs,
passing the columns to the function along with the header names??
>> 
> 
> ds2 <- lapply( ds1, na.omit)
> 
> 
>> 2. Can I easily add the sample size to each violin plotted??
> 
>> ?violplot
> No documentation for ?violplot? in specified packages and libraries:
> you could try ???violplot?
I see that I mispled that _package_ name. However, after loading it I realized
that I had no way of replicating what you are seeing, because you didn't
provide that file (or even something that resembles it. It's rather unclear
how you wanted this information presented.

-- 
David.


David Winsemius
Alameda, CA, USA

Never let it be said there's only one way to do a thing:

require(ggplot2)
require(dplyr)

#create a sample dataset
dat <- data.frame(y1=sample(c(1:10,NA),20,replace=TRUE),
                          y2=sample(c(1:10,NA),20,replace=TRUE),
                          y3=sample(c(1:10,NA),20,replace=TRUE))

# convert from wide to long
dat <- melt(dat)

# add the counts as a label
dat <- merge(dat,
          group_by(dat,variable) %>%
               summarise(lab=paste0('n=',length(na.omit(value)))))

# do the plot
ggplot(dat,aes(x=variable,y=value)) +
    geom_violin() +
    geom_text(aes(y=max(value,na.rm=TRUE)/2,label=lab))


# apologies to David Winsemius for directing this answer to him, I'll work
out how to use email one day.

On Sat, Apr 30, 2016 at 12:58 PM, Mike Smith <mike at hsm.org.uk> wrote:
> Hi
>
> First post and a relative R newbie....
>
> I am using the vioplot library to produce some violin plots. I have an
> input CSV with columns off irregular length that contain NAs. I want to
> strip the NAs out and produce a multiple violin plot automatically labelled
> using the headers. At the moment I do this
>
> Code:
> ds1 =
read.csv("http://www.lecturematerials.co.uk/data/spelling.csv")
> library(vioplot)
> y6<-na.omit(ds1$y6)
> y5<-na.omit(ds1$y5)
> y4<-na.omit(ds1$y4)
> y3<-na.omit(ds1$y3)
> y2<-na.omit(ds1$y2)
> y1<-na.omit(ds1$y1)
> vioplot(y6, y5, y4,y3,y2,y1,horizontal=TRUE, names=c("Y6",
>
"Y5","Y4","Y3","Y2","Y1"), col
= "lightblue")
>
>
> Two queries:
>
> 1. Is there a more elegant way of automatically stripping the NAs, passing
> the columns to the function along with the header names??
>
> 2. Can I easily add the sample size to each violin plotted??
>
> thanks
>
> mike
>
>
>
> ---
> Mike Smith
>
> ______________________________________________
> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
	[[alternative HTML version deleted]]

But require() should not be used interchangeably with library()... the return
value from require() should always be tested.
-- 
Sent from my phone. Please excuse my brevity.

On May 1, 2016 3:03:59 AM GMT+01:00, Tom Wright <tom at maladmin.com>
wrote:
>Never let it be said there's only one way to do a thing:
>
>require(ggplot2)
>require(dplyr)
>
>#create a sample dataset
>dat <- data.frame(y1=sample(c(1:10,NA),20,replace=TRUE),
>                          y2=sample(c(1:10,NA),20,replace=TRUE),
>                          y3=sample(c(1:10,NA),20,replace=TRUE))
>
># convert from wide to long
>dat <- melt(dat)
>
># add the counts as a label
>dat <- merge(dat,
>          group_by(dat,variable) %>%
>               summarise(lab=paste0('n=',length(na.omit(value)))))
>
># do the plot
>ggplot(dat,aes(x=variable,y=value)) +
>    geom_violin() +
>    geom_text(aes(y=max(value,na.rm=TRUE)/2,label=lab))
>
>
># apologies to David Winsemius for directing this answer to him, I'll
>work
>out how to use email one day.
>
>On Sat, Apr 30, 2016 at 12:58 PM, Mike Smith <mike at hsm.org.uk>
wrote:
>
>> Hi
>>
>> First post and a relative R newbie....
>>
>> I am using the vioplot library to produce some violin plots. I have
>an
>> input CSV with columns off irregular length that contain NAs. I want
>to
>> strip the NAs out and produce a multiple violin plot automatically
>labelled
>> using the headers. At the moment I do this
>>
>> Code:
>> ds1 =
read.csv("http://www.lecturematerials.co.uk/data/spelling.csv")
>> library(vioplot)
>> y6<-na.omit(ds1$y6)
>> y5<-na.omit(ds1$y5)
>> y4<-na.omit(ds1$y4)
>> y3<-na.omit(ds1$y3)
>> y2<-na.omit(ds1$y2)
>> y1<-na.omit(ds1$y1)
>> vioplot(y6, y5, y4,y3,y2,y1,horizontal=TRUE, names=c("Y6",
>>
"Y5","Y4","Y3","Y2","Y1"), col
= "lightblue")
>>
>>
>> Two queries:
>>
>> 1. Is there a more elegant way of automatically stripping the NAs,
>passing
>> the columns to the function along with the header names??
>>
>> 2. Can I easily add the sample size to each violin plotted??
>>
>> thanks
>>
>> mike
>>
>>
>>
>> ---
>> Mike Smith
>>
>> ______________________________________________
>> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide
>> http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>>
>
>	[[alternative HTML version deleted]]
>
>______________________________________________
>R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
>https://stat.ethz.ch/mailman/listinfo/r-help
>PLEASE do read the posting guide
>http://www.R-project.org/posting-guide.html
>and provide commented, minimal, self-contained, reproducible code.
	[[alternative HTML version deleted]]