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

> 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

>>> 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.
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

> On May 1, 2016, at 12:15 AM, Mike Smith <mike at hsm.org.uk> 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.
> 
> 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

>>>>> Mike Smith <mike at hsm.org.uk>
>>>>>     on Sun, 1 May 2016 08:15:44 +0100 writes:
    >>>> 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.

    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.