Re: [R] Removing NAs from dataframe (for use in Vioplot)

[Martin Maechler]

> Bert Gunter 
> on Mon, 2 May 2016 06:20:52 -0700 writes:

> Martin et. al.:
> na.omit(frame) will remove all rows/cases in which an NA occurs.  I'm
> not sure that this is what the OP wanted, which seemed to be to
> separately remove NA's from each column and plot the resulting column.
> This is what the lapply (and the OP's provided code) does, anyway.

> Also, lapply() produces a single list (of vectors), not a "series of 
lists" .

> Corrections happily accepted if I'm in error.

No corrections needed.  You were right ... and indeed I was
wrong in assuming that "one would want"  a complete  na.omit()
here.

Martin



> Cheers,
> Bert

> Bert Gunter

> "The trouble with having an open mind is that people keep coming along
> and sticking things into it."
> -- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )


> On Mon, May 2, 2016 at 1:49 AM, Martin Maechler
>  wrote:
>>> Mike Smith 
>>> on Sun, 1 May 2016 08:15:44 +0100 writes:
>> 
>>  On Apr 30, 2016, at 12:58 PM, Mike Smith
>>   wrote: Hi
>> 
>>  First post and a relative R newbie
>> 
>>  I am using the vioplot library to produce some violin
>>  plots.
>> 
DW> It's a package,  not a library.
>> 
>> [yes!]
>> 
>> 
>>  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)
>> 
>> 
>> > Fantastic - that does the trick! Easy when you know how!!
>> 
>> > Follow-on: is there a way feed all the lists from ds2 to
>> > vioplot? It is now a series of lists (rather than a
>> > dataframe - is that right?).
>> 
>> Yes, that's right.  So after all the above was not really
>> perfect :
>> 
>> na.omit() has been designed as a generic function and has always
>> had a method for "data.frame"; so, really
>> 
>> ds.noNA <- na.omit(ds1)
>> or  ds0NA   <- na.omit(ds1)
>> 
>> (choosing "expressive names")
>> 
>> is what you want.
>> 
>> __
>> R-help@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.

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Re: [R] Removing NAs from dataframe (for use in Vioplot)

[Bert Gunter]

Martin et. al.:

na.omit(frame) will remove all rows/cases in which an NA occurs.  I'm
not sure that this is what the OP wanted, which seemed to be to
separately remove NA's from each column and plot the resulting column.
This is what the lapply (and the OP's provided code) does, anyway.

Also, lapply() produces a single list (of vectors), not a "series of lists" .

Corrections happily accepted if I'm in error.

Cheers,
Bert


Bert Gunter

"The trouble with having an open mind is that people keep coming along
and sticking things into it."
-- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )


On Mon, May 2, 2016 at 1:49 AM, Martin Maechler
 wrote:
>> Mike Smith 
>> on Sun, 1 May 2016 08:15:44 +0100 writes:
>
>  On Apr 30, 2016, at 12:58 PM, Mike Smith
>   wrote: Hi
>
>  First post and a relative R newbie
>
>  I am using the vioplot library to produce some violin
>  plots.
>
> DW> It's a package,  not a library.
>
> [yes!]
>
>
>  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)
>
>
> > Fantastic - that does the trick! Easy when you know how!!
>
> > Follow-on: is there a way feed all the lists from ds2 to
> > vioplot? It is now a series of lists (rather than a
> > dataframe - is that right?).
>
> Yes, that's right.  So after all the above was not really
> perfect :
>
>   na.omit() has been designed as a generic function and has always
>   had a method for "data.frame"; so, really
>
> ds.noNA <- na.omit(ds1)
> or  ds0NA   <- na.omit(ds1)
>
> (choosing "expressive names")
>
> is what you want.
>
> __
> R-help@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.

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Re: [R] Removing NAs from dataframe (for use in Vioplot)

[Martin Maechler]

> Mike Smith 
> on Sun, 1 May 2016 08:15:44 +0100 writes:

 On Apr 30, 2016, at 12:58 PM, Mike Smith
  wrote: Hi

 First post and a relative R newbie

 I am using the vioplot library to produce some violin
 plots.

DW> It's a package,  not a library.

[yes!]


 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)


> Fantastic - that does the trick! Easy when you know how!!

> Follow-on: is there a way feed all the lists from ds2 to
> vioplot? It is now a series of lists (rather than a
> dataframe - is that right?).

Yes, that's right.  So after all the above was not really
perfect :

  na.omit() has been designed as a generic function and has always
  had a method for "data.frame"; so, really

ds.noNA <- na.omit(ds1)
or  ds0NA   <- na.omit(ds1)

(choosing "expressive names")

is what you want.

__
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Re: [R] Removing NAs from dataframe (for use in Vioplot)

[David Winsemius]

> On May 1, 2016, at 12:15 AM, Mike Smith  wrote:
> 
 On Apr 30, 2016, at 12:58 PM, Mike Smith  wrote:
> 
 Hi
> 
 First post and a relative R newbie
> 
 I am using the vioplot library to produce some violin plots.
> 
> DW> 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)
> 
> 
> Fantastic - that does the trick! Easy when you know how!! 
> 
> Follow-on: is there a way feed all the lists from ds2 to vioplot? It is now a 
> series of lists (rather than a dataframe - is that right?). So this works, 
> 
> library(vioplot)
> ds1 = read.csv("http://www.lecturematerials.co.uk/data/spelling.csv;)
> ds2 <- lapply( ds1, na.omit)
> vioplot(ds2$y1,ds2$y2)
> 
> but this doesnt
> 
> library(vioplot)
> ds1 = read.csv("http://www.lecturematerials.co.uk/data/spelling.csv;)
> ds2 <- lapply( ds1, na.omit)
> vioplot(ds2)
> 
Error in min(data) : invalid 'type' (list) of argument


I had trouble, too. I thought, "Oh, this is easy, just use `do.call`", but I 
failed in getting any successful argument passing that way. 

> do.call('vioplot', list(x=ds2[[6]], ds2[-6]) )
Error in min(data) : invalid 'type' (list) of argument
> do.call('vioplot', c(x=ds2[[6]], ds2[-6]) )
Error in vioplot(x1 = 5L, x2 = 10L, x3 = 6L, x4 = 7L, x5 = 7L, x6 = 6L,  : 
  argument "x" is missing, with no default

Eventually I re-wrote the first line of vioplot's body to behave the way I 
thought made the most sense:

 vioplot <- 
function (x, ..., range = 1.5, h = NULL, ylim = NULL, names = NULL, 
horizontal = FALSE, col = "magenta", border = "black", lty = 1, 
lwd = 1, rectCol = "black", colMed = "white", pchMed = 19, 
at, add = FALSE, wex = 1, drawRect = TRUE) 
{
datas <- c(list(x), ...)
#  but keep the rest the same.

# I then get success with:

vioplot(ds2[['y1']], ds2[-6])  # success

do.call('vioplot', list(x=ds2[[6]], ds2[-6]) ) # also successes
do.call('vioplot', list(x=ds2[['y1']], ds2[-6]) )

This is retracing a route explored 8 years ago:

http://markmail.org/search/?q=list%3Aorg.r-project.r-help+list+argument+to+vioplot#query:list%3Aorg.r-project.r-help%20list%20argument%20to%20vioplot+page:1+mid:j6lapgri46utcod7+state:results


It's probably easier to use that helper-function approach than my efforts at 
hacking.

Best of luck;

David


 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’
> 
> DW> I see that I mispled that _package_ name. However, after loading
> DW> it I realized that I had no way of replicating what you are
> DW> seeing, because you didn't provide that file (or even something
> DW> that resembles it. It's rather unclear how you wanted this information 
> presented.
> 
> The original code *should* have worked as the csv was online. There doesnt 
> seem to be any option in vioplot to add the sample size (these are all small 
> samples which I wanted to highlight) so I dont know if this is easily done 
> elsewhere.
> 
> Thanks again!!
> ---
> Mike Smith
> 

David Winsemius
Alameda, CA, USA

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Re: [R] Removing NAs from dataframe (for use in Vioplot)

[Mike Smith]

>>> On Apr 30, 2016, at 12:58 PM, Mike Smith  wrote:

>>> Hi

>>> First post and a relative R newbie

>>> I am using the vioplot library to produce some violin plots.

DW> 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)


Fantastic - that does the trick! Easy when you know how!! 

Follow-on: is there a way feed all the lists from ds2 to vioplot? It is now a 
series of lists (rather than a dataframe - is that right?). So this works, 

library(vioplot)
ds1 = read.csv("http://www.lecturematerials.co.uk/data/spelling.csv;)
ds2 <- lapply( ds1, na.omit)
vioplot(ds2$y1,ds2$y2)

but this doesnt

library(vioplot)
ds1 = read.csv("http://www.lecturematerials.co.uk/data/spelling.csv;)
ds2 <- lapply( ds1, na.omit)
vioplot(ds2)

>>> 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’

DW> I see that I mispled that _package_ name. However, after loading
DW> it I realized that I had no way of replicating what you are
DW> seeing, because you didn't provide that file (or even something
DW> that resembles it. It's rather unclear how you wanted this information 
presented.

The original code *should* have worked as the csv was online. There doesnt seem 
to be any option in vioplot to add the sample size (these are all small samples 
which I wanted to highlight) so I dont know if this is easily done elsewhere.

Thanks again!!
---
Mike Smith

__
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Re: [R] Removing NAs from dataframe (for use in Vioplot)

[Jeff Newmiller]

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  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  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@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@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]]

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Re: [R] Removing NAs from dataframe (for use in Vioplot)

[Tom Wright]

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  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@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]]

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Re: [R] Removing NAs from dataframe (for use in Vioplot)

[David Winsemius]

> On Apr 30, 2016, at 4:16 PM, David Winsemius  wrote:
> 
> 
>> On Apr 30, 2016, at 12:58 PM, Mike Smith  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

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] Removing NAs from dataframe (for use in Vioplot)

[David Winsemius]

> On Apr 30, 2016, at 12:58 PM, Mike Smith  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@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

__
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[R] Removing NAs from dataframe (for use in Vioplot)

[Mike Smith]

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

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