Beads Summary Plot of Ranges for R

The beadsplot function is designed for a data frame with a factor column and many observation columns.  This function summarize the data visually.  The builtin iris data is suitable to start with this function quickly, because it has a factor on 5th column, and other 4 columns are numeric observations.

Let’s make a summary table of iris data first, without using the beadsplot.

> str(iris)
'data.frame':    150 obs. of  5 variables:
 $ Sepal.Length: num  5.1 4.9 4.7 4.6 5 5.4 4.6 5 4.4 4.9 ...
 $ Sepal.Width : num  3.5 3 3.2 3.1 3.6 3.9 3.4 3.4 2.9 3.1 ...
 $ Petal.Length: num  1.4 1.4 1.3 1.5 1.4 1.7 1.4 1.5 1.4 1.5 ...
 $ Petal.Width : num  0.2 0.2 0.2 0.2 0.2 0.4 0.3 0.2 0.2 0.1 ...
 $ Species     : Factor w/ 3 levels "setosa","versicolor",..: 1 1 1 1 1 1 1 1 1 1 ...

> lapply(list(max=max, mean=mean, min=min), function(FUN)
    apply(iris[1:4], 2, function(x)
      tapply(x, iris[,5], FUN)))

$max
              Sepal.Length Sepal.Width Petal.Length Petal.Width
setosa              5.8         4.4          1.9         0.6
versicolor          7.0         3.4          5.1         1.8
virginica           7.9         3.8          6.9         2.5

$mean
              Sepal.Length Sepal.Width Petal.Length Petal.Width
setosa            5.006       3.428        1.462       0.246
versicolor        5.936       2.770        4.260       1.326
virginica         6.588       2.974        5.552       2.026

$min
              Sepal.Length Sepal.Width Petal.Length Petal.Width
setosa              4.3         2.3          1.0         0.1
versicolor          4.9         2.0          3.0         1.0
virginica           4.9         2.2          4.5         1.4

Someone may say this is enough, but I want more visuals.

beadsplot(Species~., iris, scale.mean=NULL, scale.range=NULL)

Fig. 1. raw plot of summary

Observations may have different ranges and units between columns. Eg. soil chemical component data frame may have pH, EC, Lime, Phosphoric acid, CEC and so on. These columns have quite different units.  So I need a way to separate y-axis scales by column. Let’s do the relative scaling by the whole range of each column.

beadsplot(Species~., iris, scale.mean=NULL)

Fig. 2. scaled by ranges

In Fig. 2, the y-axis has no units, and every column is scaled between -1 and 1.

Another relative scaling is using the whole mean with the range.  The mean of each column is also a useful information.

beadsplot(Species~., iris)

Fig. 3. scaled by means and ranges

Fig. 3 is very similar to Fig.2. But the y-axis is slightly shifted at each column. Now the mean of each column is located at y=0. It is showing asymmetry of ranges.

The beadsplot can be used to show summary table like the first one.

beadsplot(Species~., iris, plot=FALSE)

$scaled
, , summaries = S

              factors
series             setosa versicolor  virginica
  Sepal.Length -0.8574074 -0.5240741 -0.5240741
  Sepal.Width  -0.6311111 -0.8811111 -0.7144444
  Petal.Length -0.9349153 -0.2569492  0.2515254
  Petal.Width  -0.9161111 -0.1661111  0.1672222

, , summaries = E

              factors
series             setosa  versicolor   virginica
  Sepal.Length -0.4651852  0.05148148  0.41370370
  Sepal.Width   0.3088889 -0.23944444 -0.06944444
  Petal.Length -0.7783051  0.17016949  0.60813559
  Petal.Width  -0.7944444  0.10555556  0.68888889

, , summaries = N

              factors
series              setosa versicolor virginica
  Sepal.Length -0.02407407  0.6425926 1.1425926
  Sepal.Width   1.11888889  0.2855556 0.6188889
  Petal.Length -0.62983051  0.4549153 1.0650847
  Petal.Width  -0.49944444  0.5005556 1.0838889

attr(,"summary.labels")
                                       S 
                   ".Primitive(\"min\")" 
                                       E 
"function (x, ...)  UseMethod(\"mean\")" 
                                       N 
                   ".Primitive(\"max\")" 

$raw
, , summaries = S

              factors
series         setosa versicolor virginica
  Sepal.Length    4.3        4.9       4.9
  Sepal.Width     2.3        2.0       2.2
  Petal.Length    1.0        3.0       4.5
  Petal.Width     0.1        1.0       1.4

, , summaries = E

              factors
series         setosa versicolor virginica
  Sepal.Length  5.006      5.936     6.588
  Sepal.Width   3.428      2.770     2.974
  Petal.Length  1.462      4.260     5.552
  Petal.Width   0.246      1.326     2.026

, , summaries = N

              factors
series         setosa versicolor virginica
  Sepal.Length    5.8        7.0       7.9
  Sepal.Width     4.4        3.4       3.8
  Petal.Length    1.9        5.1       6.9
  Petal.Width     0.6        1.8       2.5

attr(,"summary.labels")
                                       S 
                   ".Primitive(\"min\")" 
                                       E 
"function (x, ...)  UseMethod(\"mean\")" 
                                       N 
                   ".Primitive(\"max\")" 

$scale
$scale$scale.range
[1] 1

$scale$scale.mean
[1] 0

$scale$scale.log
[1] FALSE

$scale$scale.data.center
NULL

$scale$scale.data.border
NULL

$scale$scale.grid.center
[1] "grey"

$scale$scale.grid.border
[1] "grey"

$scale$cex.axis
[1] 1

Download is available at http://code.google.com/p/cowares-excel-hello/downloads/list?q=label:diaplt_r .
Expected to be available at CRAN soon.