Any way to make plot points in scatterplot more transparent in R

Question

I have a 3 column matrix  plots are made by points based on column 1 and column 2 values  but colored based on column 2  6 different groups   I can successfully plot all points  however  the last plot group  group 6  which was assigned the color purple  masks the plots of the other groups  Is there a way to make the plot points more transparent   s  lt - read table       parse-output txt   sep   t    dim s    1  67124     3 x  lt - s  1   y  lt - s  2  z  lt - s  3   cols  lt - cut z  6  labels   c  pink    red    yellow    blue    green    purple    plot x  y  main   Fragment recruitment plot - FR-HIT   ylab    Percent identity   xlab    Base pair position   col   as character cols   pch 16

User · Answer

If you decide to use ggplot2  you can set transparency of overlapping points using the alpha argument   e g   library ggplot2  ggplot diamonds  aes carat  price     geom point alpha   1 40

User · Answer

Otherwise  you have function alpha in package scales in which you can directly input your vector of colors  even if they are factors as in your example    library scales  cols  lt - cut z  6  labels   c  pink    red    yellow    blue    green    purple    plot x  y  main   Fragment recruitment plot - FR-HIT         ylab    Percent identity   xlab    Base pair position         col   alpha cols  0 4   pch 16     For an alpha of 0 4  i  e  an opacity of 40

User · Answer

If you are using the hex codes  you can add two more digits at the end of the code to represent the alpha channel   E g  half-transparency red   plot 1 100  main  Example of Plot With Transparency   lines 1 100   sin 1 100 2 pi  20    col   FF000088   lwd 4  mtext  use  col   FF000088   for the lines   function

User · Answer

Transparency can be coded in the color argument as well  It is just two more hex numbers coding a transparency between 0  fully transparent  and 255  fully visible   I once wrote this function to add transparency to a color vector  maybe it is usefull here   addTrans  lt - function color trans        This function adds transparancy to a color      Define transparancy with an integer between 0 and 255     0 being fully transparant and 255 being fully visable     Works with either color and trans a vector of equal length      or one of the two of length 1     if  length color   length trans  amp  any c length color  length trans    1   stop  Vector lengths not correct     if  length color   1  amp  length trans  gt 1  color  lt - rep color length trans     if  length trans   1  amp  length color  gt 1  trans  lt - rep trans length color      num2hex  lt - function x          hex  lt - unlist strsplit  0123456789ABCDEF  split          return paste hex  x-x  16  16 1  hex x  16 1  sep            rgb  lt - rbind col2rgb color  trans    res  lt - paste     apply apply rgb 2 num2hex  2 paste collapse     sep       return res      Some examples   cols  lt - sample c  red   green   pink   100 TRUE     Fully visable  plot rnorm 100  rnorm 100  col cols pch 16 cex 4     Somewhat transparant  plot rnorm 100  rnorm 100  col addTrans cols 200  pch 16 cex 4     Very transparant  plot rnorm 100  rnorm 100  col addTrans cols 100  pch 16 cex 4

User · Answer

When creating the colors  you may use rgb and set its alpha argument   plot 1 10  col   rgb red   1  green   0  blue   0  alpha   0 5        pch   16  cex   4  points  1 10    0 4  col   rgb red   0  green   0  blue   1  alpha   0 5          pch   16  cex   4      Please see  rgb for details

[r] Any way to make plot points in scatterplot more transparent in R?

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