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.anamar...@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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> and provide commented, minimal, self-contained, reproducible code.
>
--
John Kane
Kingston ON Canada
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