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second legend in biplot

5 messages · PIKAL Petr, Jim Lemon

Original
PIKAL Petr
# 
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))
Jim Lemon
# 
Hi Petr,
Here's an attempt, using the example in biplot.princomp:

biplot(princomp(USArrests))
[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.pikal at precheza.cz> wrote:
1 day later
PIKAL Petr
# 
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
Jim Lemon
# 
Hi Petr,
Perhaps legendg in plotrix can help:

legendg(-180,600,c("State","Crime"),lty=1,col=list("black","red"),pch=3:4)

Jim
On Wed, Dec 9, 2020 at 10:31 PM PIKAL Petr <petr.pikal at precheza.cz> wrote:
PIKAL Petr
# 
Thank you Jim

I am almost sure that biplot and prcomp itself cannot do point (text) coding 
according to some factor.

The closest way to what I want to achieve is to use result from prcomp and add 
points into existing biplot, something like that

PCA <- prcomp(iris[,-5], scale=T, center=T)
biplot(PCA)
points(PCA$x[,1:2], pch=20, col=iris$Species)
But maybe tweeking the code from fviz_pca_biplot could be easier as it is 
possible to have separate legend for point colour and shape but shape and 
colour is the same.
https://stackoverflow.com/questions/47482879/how-to-make-a-pretty-biplot-in-r-without-using-external-packages

I want shape and colour coded by different factors.

Anyway, thanks for your effort.

Cheers
Petr