[R] scatter plot

[John Kane]

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
>
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-- 
John Kane
Kingston ON Canada

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