Legend in plotIndiv does not respect pch levels order

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Issue #100 resolved
Kim-Anh Le Cao repo owner created an issue

See email from André Luis Neves, June 24.

Here it is the code that didn't change the correct order of time (in days).

time = factor(map$TimeOld, levels = c("0", "80", "100", "180"))

plotIndiv(splsda.res, comp = c(1,2),
          ind.names = FALSE, 
          ellipse = TRUE, 
          legend = TRUE,
          group=Y,
          id.names=time,
          pch= time,
          pch.levels=time,
          legend.title="Breeds",
          legend.title.pch ="Time (in days)",
          title = 'Gene Families, sPLSDA comp 1 - 2') 

Comments (1)

  1. Kim-Anh Le Cao reporter

    This is an issue inherent to ggplot2 that assigns letters to factors (here the pch) inside the function. Best option is to use the

    style = 'graphics' or 'lattice'
    

    in plotIndiv.

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