[R] scatter plot

[John Kane]

In line

On Mon, 10 Feb 2020 at 15:12, Ana Marija <sokovic.anamarija using gmail.com>
wrote:

> Hi,
>
> Thanks for getting back to me. I need to have there two groups:
>
> "nPDR.rg  and "PDR.rg"
>

Your sample data only contains NoD.rg &  nPDR.rg.  To start with, I think
we need some representative data supplied in dput format just as I supplied
an "mds" dataset.  If I understand your mds$col statement correctly there
is only 22 rows of data. Just issue the command "dput(mds) and copy the
output into your e-mail. This will allow R-help readers to use the exact
same data set that you have on your computer.

>
> can you please let me know how my loop would look like just with those
> two groups
>

Well no I cannot  because I am still trying ta figure out where "d1 and d2
came from or why you need that loop. It looks like you are renaming the
columns in "mbs" three times but why? And why do it in a loop?

If all that you are doing is renaming the columns from the "ar_diff" data
set names just do it once,
colnames(mds)  <-  c("Dim.1", Dim.2, Dim.3) before you even create the
"cols" column.

We really need to see the data.

I have never used library("ggpubr") and I cannot see why cols is appearing
in the legend---well it does with my data set. Actually, given my version
of the data set I don't see why it it printing the graph.


Also do you really want all three grcaphs in one .pdf file?



> Thanks
> Ana
>
>










> On Mon, Feb 10, 2020 at 2:03 PM John Kane <jrkrideau using gmail.com> wrote:
> >
> > I must admit that I do not understand what you are doing but can you
> notm just subset the data?
> > Note I am using a data.frame not a tibble.  It would be helpful if you
> could supply sample data in dput() forest.
> >
> > library("ggpubr")
> > mds  <-  structure(list(Dim.1 = c(0.41, 0.184, 0.394, -0.49, 0.635,
> -0.723,
> > 0.76, -0.0918, -0.336, -0.439, -1.9, 0.631), Dim.2 = c(-0.984,
> > 1.11, -0.159, -0.326, -0.112, 0.153, -0.732, 0.645, 0.756, -0.557,
> > -0.858, -0.093), Dim.3 = c(-0.87, 0.101, 0.0272, 0.535, -0.0503,
> > -0.245, 0.568, -0.189, 0.12, 0.556, -0.949, 1.43), cols = c("nPDR.rg",
> > "nPDR.rg", "nPDR.rg", "nPDR.rg", "nPDR.rg", "nPDR.rg", "NoD.rg",
> > "NoD.rg", "NoD.rg", "NoD.rg", "NoD.rg", "NoD.rg")), class =
> "data.frame", row.names = c(NA,
> > -12L))
> >
> > mm1  <-  subset(mds, cols =="nPDR.rg")
> > ggscatter(mds, x = d1, y = d2, size=3, color = "red")
> >
> > On Mon, 10 Feb 2020 at 14:04, Ana Marija <sokovic.anamarija using gmail.com>
> wrote:
> >>
> >> Hello,
> >>
> >> I have a code like this:
> >>
> >> mds <- (ar_diff) %>% dist() %>% cmdscale(k=3) %>% as_tibble()
> >> mds$cols <- as.factor(c(rep("nPDR.rg",7),  rep("PDR.rg",8),
> rep("NoD.rg",7)))
> >>
> >> pdf(file = "RG.pdf")
> >>
> >>
> >> for (dim1 in 1:2){
> >>   for (dim2 in (dim1+1):3){
> >>     d1 = paste0("Dim.",dim1); d2 = paste0("Dim.",dim2)
> >>     colnames(mds)[c(dim1,dim2)] <- c(d1,d2)
> >>     print(colnames(mds))
> >>     print(ggscatter(mds, x = d1, y = d2, color ="cols" ,size=3
> >> ,palette=c("blue","red","green")))
> >>   }
> >> }
> >> dev.off()
> >>
> >> How do I run the same plot but excluding NoD.rg? What do I need to
> >> change in this for loop?
> >>
> >> > head(mds)
> >> # A tibble: 6 x 4
> >>    Dim.1  Dim.2   Dim.3 cols
> >>    <dbl>  <dbl>   <dbl> <fct>
> >> 1  1.41  -0.984 -0.870  nPDR.rg
> >> 2  0.184  1.11   0.101  nPDR.rg
> >> 3  0.394 -0.159  0.0272 nPDR.rg
> >> 4 -0.490 -0.326  0.535  nPDR.rg
> >> 5  0.635 -0.112 -0.0503 nPDR.rg
> >> 6 -0.723  0.153 -0.245  nPDR.rg
> >>
> >> > tail(mds)
> >> # A tibble: 6 x 4
> >>     Dim.1   Dim.2  Dim.3 cols
> >>     <dbl>   <dbl>  <dbl> <fct>
> >> 1  0.760  -0.732   0.568 NoD.rg
> >> 2 -0.0918  0.645  -0.189 NoD.rg
> >> 3 -0.336   0.756   0.120 NoD.rg
> >> 4 -0.439  -0.557   0.556 NoD.rg
> >> 5 -1.90   -0.858  -0.949 NoD.rg
> >> 6  0.631  -0.0930  1.43  NoD.rg
> >>
> >> Thanks
> >> Ana
> >>
> >> ______________________________________________
> >> R-help using 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.
> >
> >
> >
> > --
> > John Kane
> > Kingston ON Canada
>


-- 
John Kane
Kingston ON Canada

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