How can I plot with 2 different y-axes

Question

I would like superimpose two scatter plots in R so that each set of points has its own  different  y-axis  i e   in positions 2 and 4 on the figure  but the points appear superimposed on the same figure   Is it possible to do this with plot   Edit Example code showing the problem    example code for SO question y1  lt - rnorm 10  100  20  y2  lt - rnorm 10  1  1  x  lt - 1 10   in this plot y2 is plotted on what is clearly an inappropriate scale plot y1   x  ylim   c -1  150   points y2   x  pch   2

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One option is to make two plots side by side  ggplot2 provides a nice option for this with facet wrap     dat  lt - data frame x   c rnorm 100   rnorm 100  10  2       y   c rnorm 100   rlnorm 100  9  2       index   rep 1 2  each   100       require ggplot2  ggplot dat  aes x y      geom point      facet wrap   index  scales    free y

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update  Copied material that was on the R wiki at http   rwiki sciviews org doku php id tips graphics-base 2yaxes  link now broken  also available from the wayback machine  Two different y axes on the same plot   some material originally by Daniel Rajdl 2006 03 31 15 26   Please note that there are very few situations where it is appropriate to use two different scales on the same plot  It is very easy to mislead the viewer of the graphic  Check the following two examples and comments on this issue  example1  example2 from Junk Charts   as well as this article by Stephen Few  which concludes    I certainly cannot conclude  once and for all  that graphs with dual-scaled axes are never useful  only that I cannot think of a situation that warrants them in light of other  better solutions       Also see point  4 in this cartoon      If you are determined  the basic recipe is to create your first plot  set par new TRUE  to prevent R from clearing the graphics device  creating the second plot with axes FALSE  and setting xlab and ylab to be blank     ann FALSE should also work  and then using axis side 4  to add a new axis on the right-hand side  and mtext     side 4  to add an axis label on the right-hand side  Here is an example using a little bit of made-up data   set seed 101  x  lt - 1 10 y  lt - rnorm 10     second data set on a very different scale z  lt - runif 10  min 1000  max 10000   par mar   c 5  4  4  4    0 3     Leave space for z axis plot x  y    first plot par new   TRUE  plot x  z  type    l   axes   FALSE  bty    n   xlab       ylab       axis side 4  at   pretty range z    mtext  z   side 4  line 3    twoord plot   in the plotrix package automates this process  as does doubleYScale   in the latticeExtra package   Another example  adapted from an R mailing list post by Robert W  Baer       set up some fake test data time  lt - seq 0 72 12  betagal abs  lt - c 0 05 0 18 0 25 0 31 0 32 0 34 0 35  cell density  lt - c 0 1000 2000 3000 4000 5000 6000      add extra space to right margin of plot within frame par mar c 5  4  4  6    0 1      Plot first set of data and draw its axis plot time  betagal abs  pch 16  axes FALSE  ylim c 0 1   xlab     ylab         type  b  col  black   main  Mike s test data   axis 2  ylim c 0 1  col  black  las 1      las 1 makes horizontal labels mtext  Beta Gal Absorbance  side 2 line 2 5  box       Allow a second plot on the same graph par new TRUE      Plot the second plot and put axis scale on right plot time  cell density  pch 15   xlab     ylab     ylim c 0 7000        axes FALSE  type  b   col  red      a little farther out  line 4  to make room for labels mtext  Cell Density  side 4 col  red  line 4   axis 4  ylim c 0 7000   col  red  col axis  red  las 1      Draw the time axis axis 1 pretty range time  10   mtext  Time  Hours   side 1 col  black  line 2 5        Add Legend legend  topleft  legend c  Beta Gal   Cell Density      text col c  black   red   pch c 16 15  col c  black   red        Similar recipes can be used to superimpose plots of different types     bar plots  histograms  etc

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I too suggests  twoord stackplot   in the plotrix package plots with more of two ordinate axes   data lt -read table text   e0AL fxAL e0CO fxCO e0BR fxBR anos  51 8  5 9 50 6  6 8 51 0  6 2 1955  54 7  5 9 55 2  6 8 53 5  6 2 1960  57 1  6 0 57 9  6 8 55 9  6 2 1965  59 1  5 6 60 1  6 2 57 9  5 4 1970  61 2  5 1 61 8  5 0 59 8  4 7 1975  63 4  4 5 64 0  4 3 61 8  4 3 1980  65 4  3 9 66 9  3 7 63 5  3 8 1985  67 3  3 4 68 0  3 2 65 5  3 1 1990  69 1  3 0 68 7  3 0 67 5  2 6 1995  70 9  2 8 70 3  2 8 69 5  2 5 2000  72 4  2 5 71 7  2 6 71 1  2 3 2005  73 3  2 3 72 9  2 5 72 1  1 9 2010  74 3  2 2 73 8  2 4 73 2  1 8 2015  75 2  2 0 74 6  2 3 74 2  1 7 2020  76 0  2 0 75 4  2 2 75 2  1 6 2025  76 8  1 9 76 2  2 1 76 1  1 6 2030  77 6  1 9 76 9  2 1 77 1  1 6 2035  78 4  1 9 77 6  2 0 77 9  1 7 2040  79 1  1 8 78 3  1 9 78 7  1 7 2045  79 8  1 8 79 0  1 9 79 5  1 7 2050  80 5  1 8 79 7  1 9 80 3  1 7 2055  81 1  1 8 80 3  1 8 80 9  1 8 2060  81 7  1 8 80 9  1 8 81 6  1 8 2065  82 3  1 8 81 4  1 8 82 2  1 8 2070  82 8  1 8 82 0  1 7 82 8  1 8 2075  83 3  1 8 82 5  1 7 83 4  1 9 2080  83 8  1 8 83 0  1 7 83 9  1 9 2085  84 3  1 9 83 5  1 8 84 4  1 9 2090  84 7  1 9 83 9  1 8 84 9  1 9 2095  85 1  1 9 84 3  1 8 85 4  1 9 2100   header T   require plotrix  twoord stackplot lx data anos  rx data anos                    ldata cbind data e0AL  data e0BR  data e0CO                    rdata cbind data fxAL  data fxBR  data fxCO                    lcol c  black   red    blue                     rcol c  black   red    blue                      ltype c  l   o   b                     rtype c  l   o   b                      lylab  A  os de Vida   rylab  Hijos x Mujer                     xlab  Tiempo                    main  Mortalidad Fecundidad 1950   2100                    border  grey80   legend  bottomright   c paste  Proy                           c  A  Latina    Brasil    Colombia      cex 1          col c  black   red    blue    lwd 2  bty  n             lty c 1 1 2   pch c NA 1 1

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If you can give up the scales axis labels  you can rescale the data to  0  1  interval  This works for example for different  wiggle  trakcs on chromosomes  when you re generally interested in local correlations between the tracks and they have different scales  coverage in thousands  Fst 0-1      rescale numeric vector into  0  1  interval   clip everything outside the range  rescale  lt - function vec  lims range vec   clip c 0  1         find the coeficients of transforming linear equation     that maps the lims range to  0  1    slope  lt -  1 - 0     lims 2  - lims 1     intercept  lt - - slope   lims 1     xformed  lt - slope   vec   intercept      do the clipping   xformed xformed  lt  0   lt - clip 1    xformed xformed  gt  1   lt - clip 2     xformed     Then  having a data frame with chrom  position  coverage and fst columns  you can do something like   ggplot d  aes position        geom line aes y   rescale fst         geom line aes y   rescale coverage        facet wrap  chrom    The advantage of this is that you re not limited to two trakcs

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As its name suggests  twoord plot   in the plotrix package plots with two ordinate axes   library plotrix  example twoord plot

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Another alternative which is similar to the accepted answer by  BenBolker is redefining the coordinates of the existing plot when adding a second set of points   Here is a minimal example   Data   x   lt - 1 10 y1  lt - rnorm 10  100  20  y2  lt - rnorm 10  1  1    Plot   par mar c 5 5 5 5  0 1  las 1   plot new   plot window xlim range x   ylim range y1   points x  y1  col  red   pch 19  axis 1  axis 2  col axis  red   box    plot window xlim range x   ylim range y2   points x  y2  col  limegreen   pch 19  axis 4  col axis  limegreen

[r] How can I plot with 2 different y-axes?

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