a +1 shift overlaying lines/points on a boxplot (PR#398) - R-devel

acuster@nature.berkeley.edu

Mon, Jan 10, 2000 5:53 PM #

Full_Name: Adrian Custer
Version: 0.90.0
OS: Linux on Thinkpad (pentium) and desktop (K6)
Submission from: (NULL) (128.32.251.234)


When I create a boxplot, and then try to overlay a lowess fit or just the
points, 
the points do not appear in the highest level and the lowess curve does not
reach 
the highest level. However, if I add one to each of the models, the problem is
solved.
I tried this on two different machines, a laptop and a desktop both running 
Gnu/linux+gnome. If you can't reproduce this please let me know.  -adrian

[1]  0.629 -0.584  0.132 -0.012 -0.813 -0.291 -0.813 -0.291 -0.584 -0.164
 [11] -0.518 -0.731  0.074 -0.731  0.286  0.206 -0.257  0.608 -0.038 -0.291
 [21] -0.274 -0.274  0.402 -0.325 -0.343 -0.012  0.359 -0.038  0.675 -0.497
 [31]  0.026  0.608 -0.325  0.109  0.507  0.484 -0.149  0.368  0.227  0.086
 [41] -0.540  0.377 -0.149 -0.038  0.154  0.573  0.428  0.852  0.164  0.744
 [51]  0.061  0.080 -0.354  0.003  0.522 -0.508 -0.613 -0.271 -0.245 -0.080
 [61] -0.271 -0.651  0.265 -0.613  0.666  0.382  0.061 -0.542  0.510 -0.038
 [71] -0.443  0.042  0.764 -0.017 -0.148  0.023 -0.613 -0.148  0.354 -0.412
 [81]  0.522  0.169 -0.220  0.080  0.080  0.448  0.116 -0.059  0.061  0.185
 [91] -0.325 -0.038 -0.220 -0.325  0.151  0.903 -0.059  0.265  0.250  0.250
[101]  0.161  0.502  0.684  0.222  0.063 -0.414  0.222  0.028 -0.260 -0.046
[111] -0.360 -0.046 -0.260 -0.169 -0.169 -0.009  0.192 -0.046  0.028  0.222
[121]  0.129  0.502  0.097  0.306  0.384 -0.009 -0.532  0.028 -0.086 -0.260
[131] -0.086 -0.213 -0.471 -0.820 -0.414  0.222  0.097  0.251 -0.009  0.279
[141] -0.009  0.279 -0.260 -0.086  0.063  0.161 -0.009  0.524  0.063 -0.665
[151]  0.127  0.575  0.127  0.287  0.249 -0.301  0.287  0.127 -0.176 -0.013
[161] -0.301  0.082 -0.176 -0.370 -0.118 -0.064  0.210 -0.064  0.082 -0.064
[171]  0.169  0.546  0.036  0.392  0.323 -0.064 -0.706  0.127 -0.118 -0.236
[181] -0.013 -0.301 -0.370 -0.812 -0.524  0.210  0.392  0.036 -0.176  0.249
[191]  0.082  0.036 -0.301 -0.301 -0.013  0.127  0.127  0.752  0.127 -0.301
[201]  0.108  0.453  0.108  0.166  0.220 -0.327  0.048  0.271 -0.240 -0.086
[211] -0.422 -0.017  0.048 -0.327 -0.327 -0.086  0.166 -0.160  0.108 -0.086
[221]  0.166  0.571 -0.086  0.366  0.320 -0.017 -0.645  0.166 -0.240 -0.017
[231] -0.017 -0.240 -0.422 -0.240 -0.645  0.048  0.411 -0.017 -0.240  0.271
[241]  0.320 -0.017 -0.327 -0.160  0.220  0.108 -0.086  0.676  0.108  0.048
[251]  0.254 -0.188 -0.083  0.254  0.387 -0.188  0.012  0.387 -0.306 -0.306
[261] -0.594  0.012  0.012 -0.776 -0.440 -0.188  0.254 -0.083 -0.440 -0.188
[271]  0.323  0.448  0.099  0.505  0.323 -0.083 -0.594  0.254 -0.188 -0.083
[281]  0.012 -0.306 -0.440 -0.083 -0.306  0.012  0.448  0.099 -0.188  0.254
[291]  0.505  0.254 -0.188 -0.306  0.387  0.099  0.012  0.659  0.179  0.099

[1] 4 0 0 3 0 3 4 4 4 0 4 0 4 2 0 4 0 0 4 0 2 3 1 3 3 4 4 3 3 4 4 4 2 3 3 0 3
 [38] 0 4 3 3 2 4 3 3 4 4 1 0 0 4 0 0 3 0 3 4 4 4 0 4 0 4 2 0 4 0 0 4 0 2 3 1 3
 [75] 3 4 4 3 3 4 4 4 2 3 3 0 3 0 4 3 3 2 4 3 3 4 4 1 0 0 4 0 0 3 0 3 4 4 4 0 4
[112] 0 4 2 0 4 0 0 4 0 2 3 1 3 3 4 4 3 3 4 4 4 2 3 3 0 3 0 4 3 3 2 4 3 3 4 4 1
[149] 0 0 4 0 0 3 0 3 4 4 4 0 4 0 4 2 0 4 0 0 4 0 2 3 1 3 3 4 4 3 3 4 4 4 2 3 3
[186] 0 3 0 4 3 3 2 4 3 3 4 4 1 0 0 4 0 0 3 0 3 4 4 4 0 4 0 4 2 0 4 0 0 4 0 2 3
[223] 1 3 3 4 4 3 3 4 4 4 2 3 3 0 3 0 4 3 3 2 4 3 3 4 4 1 0 0 4 0 0 3 0 3 4 4 4
[260] 0 4 0 4 2 0 4 0 0 4 0 2 3 1 3 3 4 4 3 3 4 4 4 2 3 3 0 3 0 4 3 3 2 4 3 3 4
[297] 4 1 0 0

Thanks for your consideration and thanks a million for all the work. R is a
pleasure 
to work with. 

Best in the new year,
adrian custer
acuster@nature.berkeley.edu

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Peter Dalgaard

Wed, Jan 12, 2000 10:02 AM #

acuster@nature.berkeley.edu writes:

...

.....

Boxplot expects a *factor* as the grouping criterion. The x axis
labels are the group names, not x coordinates (i.e. it might as well
be "married, unmarried, divorced" as "0, 1, 2."), and since factors
are internally coded as 1:nlevels, that's the value used for the
actual coordinate system.

Passing a numeric vector gets it converted to a factor before use, so
things are as you should expect. Except possibly for two issues:

a) should one really do the numeric->factor conversion without a
warning message?

b) perhaps boxplot could use an at= argument saying "plot boxes here"
since the current version wouldn't be able to deal with
non-equidistant groups.

O__  ---- Peter Dalgaard             Blegdamsvej 3  
  c/ /'_ --- Dept. of Biostatistics     2200 Cph. N   
 (*) \(*) -- University of Copenhagen   Denmark      Ph: (+45) 35327918
~~~~~~~~~~ - (p.dalgaard@biostat.ku.dk)             FAX: (+45) 35327907
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Martin Maechler

Thu, Jan 13, 2000 9:36 AM #

<....>

    PD> Boxplot expects a *factor* as the grouping criterion. The x axis
    PD> labels are the group names, not x coordinates (i.e. it might as well
    PD> be "married, unmarried, divorced" as "0, 1, 2."), and since factors
    PD> are internally coded as 1:nlevels, that's the value used for the
    PD> actual coordinate system.

    PD> Passing a numeric vector gets it converted to a factor before use, so
    PD> things are as you should expect. Except possibly for two issues:

    PD> a) should one really do the numeric->factor conversion without a
    PD> warning message?

Yes, we should have that warning (and more!):

Warning messages that I am extremely missing are in the following two examples

  plot(1);  points(2,2)

  plot(1);  text(2,2,"bla")

(and similar with lines and all kinds of plots).

We *definitely* should warn the user that (s)he is drawing outside the plot
region.  
We need "graphical warnings" 
   (which can be turned off via an options() or par() call).

    PD> b) perhaps boxplot could use an at= argument saying "plot boxes here"
    PD> since the current version wouldn't be able to deal with
    PD> non-equidistant groups. 
oh yes!
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