How to give color to each class in scatter plot in R

Question

In a dataset  I want to take two attributes and create supervised scatter plot  Does anyone know how to give different color to each class     I am trying to use col    c  red   blue   yellow   in the plot command but not sure if it is right as if I include one more color  that color also comes in the scatter plot even though I have only 3 classes   Thanks

User · Answer

This article is old  but I spent a hot minute trying to figure this out so I figured I would post an updated response  My main source is this wonderful PowerPoint  http   www lrdc pitt edu maplelab slides 14-Plotting pdf  Okay  here s what I did  In this example  my data set is called  Data  and I was comparing  Touch  data against  Gaze  data  The subjects were divided into two groups   Red  and  Blue    plot Data Touch Data Category     quot Blue quot    Data Gaze Data Category     quot Blue quot    main    quot Touch v Gaze quot   xlab    quot Gaze s  quot   ylab    quot Touch  s  quot   col    quot blue quot   pch   20     This set of code creates a scatterplot of Touch v Gaze of my Blue group par new   TRUE   This tells R to create a new plot  This second plot is laid over the first automatically by R when you run all the code together plot Data Touch Data Category     quot Red quot    Data Gaze Data Category     quot Red quot    axes   FALSE  xlab    quot  quot   ylab    quot  quot   col    quot red quot   pch   2   This is the second plot  I found when I was coding these that R didn t just lay over the data points onto the Blue plot  but it also lay the axes  axes titles  and main title   To get rid of the annoying overlap problem  I used the axes function to get rid of the axes themselves and set the titles to be blank  legend x   60  y   50  legend   c  quot Blue quot    quot Red quot    col   c  quot blue quot    quot red quot    pch   c 20  2    Adding a pretty legend to round out the project   This way may be a bit longer than the pretty ggplots but I did not want to learn something completely new today  hope this helps someone

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One way is to use the lattice package and xyplot     R gt  DF  lt - data frame x 1 10  y rnorm 10  5     gt                   z sample letters 1 3   10  replace TRUE   R gt  DF     x       y z 1   1 3 91191 c 2   2 4 57506 a 3   3 3 16771 b 4   4 5 37539 c 5   5 4 99113 c 6   6 5 41421 a 7   7 6 68071 b 8   8 5 58991 c 9   9 5 03851 a 10 10 4 59293 b R gt  with DF  xyplot y   x  group z     By giving explicit grouping information via variable z  you obtain different colors  You can specify colors etc  see the lattice documentation   Because z here is a factor variable for which we obtain the levels     numeric indices   you can also do   R gt  with DF  plot x  y  col z     but that is less transparent  to me  at least    then xyplot   et al

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Here is an example that I built based on this page   library e1071   library ggplot2   mysvm       lt - svm Species      iris  Predicted   lt - predict mysvm  iris   mydf   cbind iris  Predicted  qplot Petal Length  Petal Width  colour   Species  shape   Predicted      data   iris    This gives you the output  You can easily spot the misclassified species from this figure

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Assuming the class variable is z  you can use                  with df  plot x  y  col   z     however  it s important that z is a factor variable  as R internally stores factors as integers    This way  1 is  black   2 is  red   3 is  green

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Here is how I do it in 2018  Who knows  maybe an R newbie will see it one day and fall in love with ggplot2   library ggplot2   ggplot data   iris  aes Petal Length  Petal Width  color   Species       geom point       scale color manual values   c  setosa     red    versicolor     blue    virginica     yellow

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Here is a solution using traditional graphics  and Dirk s data     gt  DF  lt - data frame x 1 10  y rnorm 10  5  z sample letters 1 3   10  replace TRUE     gt  DF     x        y z 1   1 6 628380 c 2   2 6 403279 b 3   3 6 708716 a 4   4 7 011677 c 5   5 6 363794 a 6   6 5 912945 b 7   7 2 996335 a 8   8 5 242786 c 9   9 4 455582 c 10 10 4 362427 a  gt  attach DF   plot x  y  col c  red   blue   green   z    detach DF    This relies on the fact that DF z is a factor  so when subsetting by it  its values will be treated as integers  So the elements of the color vector will vary with z as follows    gt  c  red   blue   green   DF z    1   green   blue    red     green   red     blue    red     green   green   red        You can add a legend using the legend function   legend x  topright   legend   levels DF z   col c  red   blue   green    pch 1

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If you have the classes separated in a data frame or a matrix  then you can use matplot   For example  if we have  dat lt -as data frame cbind c 1 2 5 7  c 2 1 4 2 -0 5 1  c 9 3 6 2 718     plot new   plot window c 0 nrow dat   range dat   matplot dat col c  red   blue   yellow   pch 20    Then you ll get a scatterplot where the first column of dat is plotted in red  the second in blue  and the third in yellow   Of course  if you want separate x and y values for your color classes  then you can have datx and daty  etc   An alternate approach would be to tack on an extra column specifying what color you want  or keeping an extra vector of colors  filling it iteratively with a for loop and some if branches    For example  this will get you the same plot   dat lt -as data frame      cbind c 1 2 5 7 2 1 4 2 -0 5 1 9 3 6 2 718       c rep  red  4  rep  blue  4  rep  yellow  4      dat  1  as numeric dat  1    This is necessary because                              the second column consisting of strings confuses R                              into thinking that the first column must consist of strings  too plot dat  1  pch 20 col dat  2

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