Hi all,
I am a bit confused with ggplot2. I plotted my data and have some missing data in the plot but not at the legend. I actually have 40 groups (FID) to be plotted and some are missing. My code is:
Data48a <- read.table("Data48a.eigenvec", header = T, sep = "")
PlotData48a <- ggplot(Data48a, aes(x= PC1,y= PC2, group= FID, shape= FID, color= FID))
PlotData48a+geom_point(aes(color=FID))+geom_hline(aes(yintercept=0))+ geom_vline(aes(xintercept=0))+scale_shape_manual(values=1:nlevels(Data48a$FID))+ scale_color_manual(values=1:nlevels(Data48a$FID))+coord_equal(ratio = 1)
and here is the error:
There were 50 or more warnings (use warnings() to see the first 50) . . . 49: In grid.Call.graphics(L_points, x$x, x$y, x$pch, x$size) : unimplemented pch value '28' 50: In grid.Call.graphics(L_points, x$x, x$y, x$pch, x$size) : unimplemented pch value '28'
My data is like:
FID IID PC1 PC2 PC3
Ami AX-AM-013607-1-01 0.0302889 -0.0236855 0.0294569
Ami AX-AM-013608-1-01 0.0346382 -0.0232841 0.0175366
Ami AX-AM-013609-1-01 0.0396438 -0.0157996 0.0163948
Ami AX-AM-013610-1-01 0.0386903 -0.017313 0.0146025
Ami AX-AM-013611-1-01 0.0382764 -0.0151733 0.0222798
Ami AX-AM-013613-1-01 0.0416853 -0.00826403 0.0245685
Ami AX-AM-013614-1-01 0.0388888 -0.0113679 0.0281065
Ami AX-AM-013615-1-01 0.0438035 -0.0102871 0.0156296
Ami AX-AM-013616-1-01 0.0364263 -0.0211585 0.0246802
BatakKaro ID-KR-000001-1-01 0.0321929 0.00520535 0.00480784
BatakKaro ID-KR-000002-1-01 0.0345291 -0.00101008 -0.00264379
BatakKaro ID-KR-000012-1-01 0.0352078 -0.000998926 -0.00847158
BatakKaro ID-KR-000014-1-01 0.0306035 -0.00150602 -0.00365927
Thank you
Hi Devon Ryan,
Thanks for the answer and thus I have more questions: 1. I have another data that contains more than 60 groups and why only 5 of them were not present in the plot if there are only 26 symbols? 2. If by combining color with shape we get so many possibility of dot reprensentations, why the missing dots in the plot?
Thank you
My guess is that at some point the
pch
(the symbol IDs) values start wrapping around (one would have to check the R code).