How to overlay density plots in R

Question

I would like to overlay 2 density plots on the same device with R  How can I do that  I searched the web but I didn t find any obvious solution  My idea would be to read data from a text file  columns  and then use plot density MyData Column1   plot density MyData Column2   add T   Or something in this spirit

User · Answer

Whenever there are issues of mismatched axis limits, the right tool in base graphics is to use matplot. The key is to leverage the from and to arguments to density.default. It's a bit hackish, but fairly straightforward to roll yourself:

set.seed(102349)
x1 = rnorm(1000, mean = 5, sd = 3)
x2 = rnorm(5000, mean = 2, sd = 8)

xrng = range(x1, x2)

#force the x values at which density is
#  evaluated to be the same between 'density'
#  calls by specifying 'from' and 'to'
#  (and possibly 'n', if you'd like)
kde1 = density(x1, from = xrng[1L], to = xrng[2L])
kde2 = density(x2, from = xrng[1L], to = xrng[2L])

matplot(kde1$x, cbind(kde1$y, kde2$y))

Add bells and whistles as desired (matplot accepts all the standard plot/par arguments, e.g. lty, type, col, lwd, ...).

User · Answer

You can use the ggjoy package  Let s say that we have three different beta distributions such as  set seed 5  b1 lt -data frame Variant   quot Variant 1 quot   Values   rbeta 1000  101  1001   b2 lt -data frame Variant   quot Variant 2 quot   Values   rbeta 1000  111  1011   b3 lt -data frame Variant   quot Variant 3 quot   Values   rbeta 1000  11  101     df lt -rbind b1 b2 b3   You can get the three different distributions as follows  library tidyverse  library ggjoy    ggplot df  aes x Values  y Variant        geom joy scale   2  alpha 0 5        scale y discrete expand c 0 01  0         scale x continuous expand c 0 01  0         theme joy

User · Answer

Adding base graphics version that takes care of y-axis limits  add colors and works for any number of columns   If we have a data set   myData  lt - data frame std nromal rnorm 1000  m 0  sd 1                        wide normal rnorm 1000  m 0  sd 2                        exponent rexp 1000  rate 1                        uniform runif 1000  min -3  max 3                           Then to plot the densities   dens  lt - apply myData  2  density   plot NA  xlim range sapply dens        x     ylim range sapply dens        y     mapply lines  dens  col 1 length dens    legend  topright   legend names dens   fill 1 length dens     Which gives

User · Answer

I took the above lattice example and made a nifty function  There is probably a better way to do this with reshape via melt cast   Comment or edit if you see an improvement    multi density plot function data main paste names data  collapse     vs              combines multiple density plots together when given a list   df data frame      for n in names data        idf data frame x data  n   label rep n length data  n          df rbind df idf        densityplot  x data df groups   label plot points   F  ref   T  auto key   list space    right   main main          Example usage   multi density plot list BN1 bn1 V1 BN2 bn2 V1  main  BN1 vs BN2    multi density plot list BN1 bn1 V1 BN2 bn2 V1

User · Answer

That s how I do it in base  it s actually mentionned in the first answer comments but I ll show the full code here  including legend as I can not comment yet      First you need to get the info on the max values for the y axis from the density plots  So you need to actually compute the densities separately first  dta A  lt - density VarA  na rm   TRUE  dta B  lt - density VarB  na rm   TRUE    Then plot them according to the first answer and define min and max values for the y axis that you just got   I set the min value to 0   plot dta A  col    blue   main    2 densities on one plot          ylim   c 0  max dta A y dta B y      lines dta B  col    red     Then add a legend to the top right corner  legend  topright   c  VarA   VarB    lty   c 1 1   col   c  blue   red

User · Answer

ggplot2 is another graphics package that handles things like the range issue Gavin mentions in a pretty slick way  It also handles auto generating appropriate legends and just generally has a more polished feel in my opinion out of the box with less manual manipulation    library ggplot2    Sample data dat  lt - data frame dens   c rnorm 100   rnorm 100  10  5                        lines   rep c  a    b    each   100    Plot  ggplot dat  aes x   dens  fill   lines     geom density alpha   0 5

User · Answer

use lines for the second one   plot density MyData Column1   lines density MyData Column2     make sure the limits of the first plot are suitable  though

User · Answer

Just to provide a complete set  here s a version of Chase s answer using lattice   dat  lt - data frame dens   c rnorm 100   rnorm 100  10  5                        lines   rep c  a    b    each   100    densityplot  dens data dat groups   lines              plot points   FALSE  ref   TRUE               auto key   list space    right      which produces a plot like this

[r] How to overlay density plots in R?

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