Colouring plot by factor in R

Question

I am making a scatter plot of two variables and would like to colour the points by a factor variable  Here is some reproducible code   data  lt - iris plot data Sepal Length  data Sepal Width  col data Species    This is all well and good but how do I know what factor has been coloured what colour

User · Answer

The lattice library is another good option   Here I ve added a legend on the right side and jittered the points because some of them overlapped   xyplot Sepal Width   Sepal Length  group Species  data iris          auto key list space  right            jitter x TRUE  jitter y TRUE

User · Answer

data lt -iris plot data Sepal Length  data Sepal Width  col data Species  legend 7 4 3 unique data Species  col 1 length data Species  pch 1    should do it for you  But I prefer ggplot2 and would suggest that for better graphics in R

User · Answer

The col argument in the plot function assign colors automatically to a vector of integers   If you convert iris Species to numeric  notice you have a vector of 1 2 and 3s So you can apply this as   plot iris Sepal Length  iris Sepal Width  col as numeric iris Species     Suppose you want red  blue and green instead of the default colors  then you can simply adjust it    plot iris Sepal Length  iris Sepal Width  col c  red    blue    green   as numeric iris Species      You can probably see how to further modify the code above to get any unique combination of colors

User · Answer

Like Maiasaura  I prefer ggplot2  The transparent reference manual is one of the reasons   However  this is one quick way to get it done    require ggplot2  data diamonds  qplot carat  price  data   diamonds  colour   color    example taken from Hadley s ggplot2 book   And cause someone famous said  plot related posts are not complete without the plot  here s the result     Here s a couple of references   qplot R example  note basically this uses the same diamond dataset I use  but crops the data before to get better performance   http   ggplot2 org book  the manual  http   docs ggplot2 org current

User · Answer

There are two ways that I know of to color plot points by factor and then also have a corresponding legend automatically generated  I ll give examples of both    Using ggplot2  generally easier  Using R s built in plotting functionality in combination with the colorRampPallete function  trickier  but many people prefer need R s built-in plotting facilities    For both examples  I will use the ggplot2 diamonds dataset  We ll be using the numeric columns diamond carat and diamond price  and the factor categorical column diamond color  You can load the dataset with the following code if you have ggplot2 installed   library ggplot2  data diamonds    Using ggplot2 and qplot  It s a one liner  Key item here is to give qplot the factor you want to color by as the color argument  qplot will make a legend for you by default   qplot    x   carat    y   price    data   diamonds    color   diamonds color   color by factor color  I know  confusing      Your output should look like this    Using R s built in plot functionality  Using R s built in plot functionality to get a plot colored by a factor and an associated legend is a 4-step process  and it s a little more technical than using ggplot2   First  we will make a colorRampPallete function  colorRampPallete   returns a new function that will generate a list of colors  In the snippet below  calling color pallet function 5  would return a list of 5 colors on a scale from red to orange to blue   color pallete function  lt - colorRampPalette    colors   c  red    orange    blue      space    Lab    Option used when colors do not represent a quantitative scale       Second  we need to make a list of colors  with exactly one color per diamond color  This is the mapping we will use both to assign colors to individual plot points  and to create our legend   num colors  lt - nlevels diamonds color  diamond color colors  lt - color pallet function num colors    Third  we create our plot  This is done just like any other plot you ve likely done  except we refer to the list of colors we made as our col argument  As long as we always use this same list  our mapping between colors and diamond colors will be consistent across our R script   plot    x   diamonds carat    y   diamonds price    xlab    Carat     ylab    Price     pch   20    solid dots increase the readability of this data plot   col   diamond color colors diamonds color      Fourth and finally  we add our legend so that someone reading our graph can clearly see the mapping between the plot point colors and the actual diamond colors   legend    x   topleft     legend   paste  Color   levels diamonds color      for readability of legend   col   diamond color colors    pch   19    same as pch 20  just smaller   cex    7   scale the legend to look attractively sized     Your output should look like this    Nifty  right

User · Answer

The command palette tells you the colours and their order when col   somefactor   It can also be used to set the colours as well   palette    1   black     red       green3    blue      cyan      magenta   yellow    gray       In order to see that in your graph you could use a legend     legend  topright   legend   levels iris Species   col   1 3  cex   0 8  pch   1    You ll notice that I only specified the new colours with 3 numbers   This will work like using a factor   I could have used the factor originally used to colour the points as well   This would make everything logically flow together    but I just wanted to show you can use a variety of things   You could also be specific about the colours   Try  rainbow for starters and go from there   You can specify your own or have R do it for you   As long as you use the same method for each you re OK

[r] Colouring plot by factor in R

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