Thank you Jim.
biplot can have distinct colours of points and arrows but not points coded
according to some factor. In simple example I provided, points are coded
according by 2 factors. What I would like to achieve is to colour points and
have their shapes coded by second factor, which fviz_pca_biplot does, however
it does not present this second factor in the legend.
Probably the last resort is to rewrite original code which I would like to
avoid as I am not so experienced in grid graphics.
Best regards
Petr
> -----Original Message-----
> From: Jim Lemon <drjimle...@gmail.com>
> Sent: Monday, December 7, 2020 9:53 PM
> To: PIKAL Petr <petr.pi...@precheza.cz>
> Cc: R mailing list <r-help@r-project.org>
> Subject: Re: [R] second legend in biplot
>
> Hi Petr,
> Here's an attempt, using the example in biplot.princomp:
>
> biplot(princomp(USArrests))
> > par("usr")
> [1] -497.2263 624.8856 -497.2263 624.8856
> legend(-180,600,c("State","Crime"),lty=1,col=c("black","red"))
>
> Jim
>
> On Mon, Dec 7, 2020 at 6:23 PM PIKAL Petr <petr.pi...@precheza.cz> wrote:
> >
> > Dear all
> >
> > I try to make fviz_pca_biplot with 2 (or more) legends. Below is data
> > and the code, which gives one legend (colour) for coating variable and
> > correctly shows triangles and circles for size variable. But this is
> > not shown in the legend. Hopefully somebody could help.
> >
> > And before you ask, I tried to contact maintainer about a week ago but
> > did not get response, therefore I try to post again here.
> >
> > Even an answer that current version of fviz_pca_biplot does not
> > support 2 legends with different point shapes is OK as it will send me
> > either to adapt source code or to stop trying impossible.
> >
> > Best regards
> > Petr
> >
> > library(factoextra)
> > library(FactoMineR)
> >
> > fit <- PCA(temp, quali.sup=c(9,10))
> > fviz_pca_biplot(fit, col.ind = temp$coating, repel=T, col.var =
> > "black", palette = "lancet", invisible="quali", pointsize=5,
> > pointshape=temp$size, legend.title = list(col = "Coating",
> > shape="Size"), xlim=c(-6,6), title="Instillation results")
> >
> > temp <- structure(list(leukocyte28 = c(96875L, 73438L, 68229L, 94479L,
> > 76563L, 141667L, 111042L, 93333L, 132083L, 103542L, 61667L, 77708L ),
> > macrophage28 = c(60.29, 99.13, 97.04, 98.54, 98.46, 75.2, 89.71, 98,
> > 82, 98.83, 99.08, 98.54), pmn28 = c(38.58, 0.58, 2.71, 0.92, 1, 24.25,
> > 9.29, 1.5, 15.08, 0.92, 0.67, 1), lymphocyte28 = c(1.13, 0.29, 0.25,
> > 0.54, 0.54, 0.55, 1, 0.5, 2.92, 0.25, 0.25, 0.46),
> > leukocyte3 = c(186042L, 111250L, 114375L, 111146L, 98854L,
> > 156250L, 250625L, 183125L, 202917L, 161875L, 184792L, 128333L
> > ), macrophage3 = c(53.88, 95.96, 98.29, 98.92, 98.92, 78.3,
> > 82.33, 97.83, 84.79, 97.25, 97.75, 98.46), pmn3 = c(44.75,
> > 3.46, 1.29, 0.67, 0.71, 20.4, 16.67, 1.92, 14.04, 1.92, 1.67,
> > 1.21), lymphocyte3 = c(1.38, 0.58, 0.42, 0.42, 0.38, 1.3,
> > 1, 0.25, 1.17, 0.83, 0.58, 0.33), coating = structure(c(3L,
> > 3L, 3L, 1L, 7L, 1L, 2L, 5L, 4L, 6L, 3L, 3L), .Label = c("alumina",
> > "both", "none", "phosphate", "silica", "tungsten", "zirconia"
> > ), class = "factor"), size = structure(c(1L, 1L, 2L, 2L,
> > 2L, 1L, 2L, 1L, 2L, 1L, 2L, 2L), .Label = c("nano", "pigmentary"
> > ), class = "factor")), class = "data.frame", row.names = c(NA,
> > 12L))
> >
> > ______________________________________________
> > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
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> > PLEASE do read the posting guide
> > http://www.R-project.org/posting-guide.html
> > and provide commented, minimal, self-contained, reproducible code.
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