Repel labels in PLOT.RDA function

[magibc]

Dear @michaelgreenacre

First of all, thank you for you R package easyCODA and your collaboration team (coda4microbiome).

In my microbiota study I'm trying to plot an RDA using PLOT.RDA() function.

PLOT.RDA(provaRDA2, map="symmetric", colrows = colcat[diagnosis] , colcats=colcat, rescale = 1, indcat = 1:11, pchrows = rep(19, nrow(x_no0)), cexs = c(1,1,1), fonts = c(2,4,2))

Nevertheless, the names of species appears overlapped. It is possible to use geom_text_repel(). I tried without success indicanting me the following error when I tried to use geom_text_repel() function.

Error in `validate_mapping()`:
! `mapping` must be created by `aes()`
Run `rlang::last_error()` to see where the error occurred.

Thanks on advance,

Magí.

[michaelgreenacre]

Hi Magi

This is a typical problem, overlapping labels. I see two solutions for you.

1. You export the coordinates of the rows, columns and covariates (looks like categories in your case). These are in your RDA object provaRDA2, usually you would plot the row principal coordinates in $rowpcoord, the column standard coordinates in $colcoord, and the covariates in $covcoord. You will probably have to introduce scale factors for the columns and the covariates. So your use ggplot2 and its options then, and you have complete control over colours, symbols, labels, etc...
2. You edit the map to de-overlap the labels manually (I usually do this since I don't use ggplot2). That is, export the PLOT.RDA map to PDF and use a PDF editor (I use the free one Inkscape, but you might have Adobe Illustrator...). Then shift labels very slightly to avoid the overlapping.

Best wishes Michael

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On Sat, 13 Aug 2022 at 10:55, magibc @.***> wrote:

Dear @michaelgreenacre https://github.com/michaelgreenacre

First of all, thank you for you R package easyCODA and your collaboration team (coda4microbiome).

In my microbiota study I'm trying to plot an RDA using PLOT.RDA() function.

PLOT.RDA(provaRDA2, map="symmetric", colrows = colcat[diagnosis] , colcats=colcat, rescale = 1, indcat = 1:11, pchrows = rep(19, nrow(x_no0)), cexs = c(1,1,1), fonts = c(2,4,2))

Nevertheless, the names of species appears overlapped. It is possible to use geom_text_repel(). I tried without success indicanting me the following error when I tried to use geom_text_repel() function.

Error in validate_mapping():

! mapping must be created by aes()

Run rlang::last_error() to see where the error occurred.

Thanks on advance,

Magí.

— Reply to this email directly, view it on GitHub https://github.com/michaelgreenacre/CODAinPractice/issues/1, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACXFPFGZPFE6ANSQSUYKLYLVY5PI3ANCNFSM56NZ4MNA . You are receiving this because you were mentioned.Message ID: @.***>

[magibc]

Thank you Michael. Sorry for the delay of my response.