Hallo Mahmood
I recently struggled with similar problem useing factoextra package. You
could fiddle with xlim and ylim to set size of plot and col.ind to set the
colour.
Another option is to use prcomp function to generate data and fine tune
biplot.
See parameters expand, xlim and ylim for biplot size and points to add
points with different shape, colour and/or size.
Below is example with factoextra
Cheers
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))
> -----Original Message-----
> From: R-help <r-help-boun...@r-project.org> On Behalf Of Mahmood
> Naderan-Tahan
> Sent: Friday, February 5, 2021 4:45 PM
> To: r-help@r-project.org
> Subject: [R] Customizing plot
>
>
> Hi,
> 1- How can I assign different colors to different observations in the PCA
> chart? Assume, I have 10 observations and I want to use black color for
the
> first 5 and read for the next 5 observations.
>
> Currently, I use
>
> res.pca = PCA(mydata[,1:37], scale.unit=TRUE, graph=T)
> plot(res.pca,axes=c(1,2))
>
>
>
> 2- How can I change the plot area size and font sizes? With these commands
>
> dev.new(width=20, height=4)
> plot(res.pca,axes=c(1,2))
>
> The final plot is not what I expected. Please see the picture
> at https://imgur.com/UINTnv7
>
>
>
>
>
> Regards,
> Mahmood
>
>
> ______________________________________________
> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
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> and provide commented, minimal, self-contained, reproducible code.
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