R help - Feb 2021 - 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

On 05/02/2021 10:44 a.m., Mahmood Naderan-Tahan wrote:
> 
> 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
No need to post twice.  You probably didn't get an answer the first time 
because it was just an hour ago, and you didn't include "mydata"
(or a
suitable subset) in your posting.  For the best chance at getting a 
helpful answer, post code that others can run.

Duncan Murdoch

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-bounces at r-project.org> On Behalf Of Mahmood
> Naderan-Tahan
> Sent: Friday, February 5, 2021 4:45 PM
> To: r-help at 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
> 
> 
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