the bar width of barchart plot in lattice package

Dear R users,

I am trying to use the following code to make a barchar plot. The  
bars in
the plot turn out to be a little narrow. Is there any way to modify  
the
width of the bars? Thank you!

library(lattice)
scores = gl(2, 5, label=c('Sensitivity', 'PPV'), length = 100)
sequences = gl(5, 1, label=c('Lemna minor', 'Dugesia japonica A',
'Gymnosporangium sabinae', 'Hymeniacidon sanguinea', 'Streptomyces
griseus'), length = 100)
levels = gl(10, 10, label = c('Cycle 1', 'Cycle 2', 'Cycle 3',  
'Cycle 4',
'Order 1', 'Order 2', 'Order 3', 'MaxPairs = 20', 'MaxPairs = Average
Length', 'MaxPairs = 500'))
factors = c(rep('Cycles', 40), rep('Order', 30), rep('MaxPairs', 30))
values = rnorm(100) # this is toy data
a = data.frame(values, scores, sequences, levels, factors)
bc.factors =
 barchart(values ~ sequences | scores * factors , data = a,
          groups = levels,
          layout = c(2,3),
          between = list(y=0.5),
          clip = list(strip = 'off'),
          par.strip.text = list(cex=0.7),
          par.settings = list(fontsize=list(text=8)),
          auto.key = list(rectangles = TRUE, space = 'right',  
columns = 1),
          draw.key = TRUE,
          scales = list(x = list(rot = 45)))

?barchart

Looking at the arguments to barchart in the help page I would have  
guessed that box.ratio would do what you want. Since that is clearly  
not reproducible code , (in the absence of test dataset of the  
appropriate structure) I suppose guessing will remain the level of my  
knowledge in this instance.

-- 
Best,
Zhenjiang

David Winsemius, MD
West Hartford, CT

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I tried that. It seems the bar width is already maximized, although  
there is a lot of space between groups of bars. Thank you anyway.

I apologize. It was reproducible code. I missed the "values"  
assignment. There is also a box.width argument which does affect how  
the plot gets drawn, but the effects do not appear salutory. It  
appears that the alignment of the bars gets shifted relative to the  
labels. The barchart function cannot seem to deal with the completity  
of the 2 * 5 factor crossed with a c(3,3,4) factor. On the other hand  
that problem seems to be present in the original plot as well. Maybe  
you should re-think the structure of the data?

Compare:

bc.factors <-
  barchart(values ~ sequences | scores * factors , data = a,
          groups = levels,
          layout = c(2,3), box.ratio=1, box.width=1.5,
          between = list(y=0.5),
          clip = list(strip = 'off'),
          par.strip.text = list(cex=0.7),
          par.settings = list(fontsize=list(text=8)),
          auto.key = list(rectangles = TRUE, space = 'right', columns  
= 1),
          draw.key = TRUE,
          scales = list(x = list(rot = 45)))

David.


>
> On Tue, Apr 20, 2010 at 10:16 AM, David Winsemius <dwinsemius at comcast.net 
> > wrote:
>
> On Apr 20, 2010, at 9:46 AM, zhenjiang xu wrote:
>
> Dear R users,
>
> I am trying to use the following code to make a barchar plot. The  
> bars in
> the plot turn out to be a little narrow. Is there any way to modify  
> the
> width of the bars? Thank you!
>
> library(lattice)
> scores = gl(2, 5, label=c('Sensitivity', 'PPV'), length = 100)
> sequences = gl(5, 1, label=c('Lemna minor', 'Dugesia japonica A',
> 'Gymnosporangium sabinae', 'Hymeniacidon sanguinea', 'Streptomyces
> griseus'), length = 100)
> levels = gl(10, 10, label = c('Cycle 1', 'Cycle 2', 'Cycle 3',  
> 'Cycle 4',
> 'Order 1', 'Order 2', 'Order 3', 'MaxPairs = 20', 'MaxPairs = Average
> Length', 'MaxPairs = 500'))
> factors = c(rep('Cycles', 40), rep('Order', 30), rep('MaxPairs', 30))
> values = rnorm(100) # this is toy data
> a = data.frame(values, scores, sequences, levels, factors)
> bc.factors =
>  barchart(values ~ sequences | scores * factors , data = a,
>          groups = levels,
>          layout = c(2,3),
>          between = list(y=0.5),
>          clip = list(strip = 'off'),
>          par.strip.text = list(cex=0.7),
>          par.settings = list(fontsize=list(text=8)),
>          auto.key = list(rectangles = TRUE, space = 'right', columns  
> = 1),
>          draw.key = TRUE,
>          scales = list(x = list(rot = 45)))
>
>
> ?barchart
>
> Looking at the arguments to barchart in the help page I would have  
> guessed that box.ratio would do what you want. Since that is clearly  
> not reproducible code , (in the absence of test dataset of the  
> appropriate structure) I suppose guessing will remain the level of  
> my knowledge in this instance.
>
>
> -- 
> Best,
> Zhenjiang
>
> David Winsemius, MD
> West Hartford, CT
>
>
>
>
> -- 
> Best,
> Zhenjiang

David Winsemius, MD
West Hartford, CT

On Apr 21, 2010, at 9:51 PM, zhenjiang xu wrote:

I tried that. It seems the bar width is already maximized, although there
is a lot of space between groups of bars. Thank you anyway.

I apologize. It was reproducible code. I missed the "values" assignment.
There is also a box.width argument which does affect how the plot gets
drawn, but the effects do not appear salutory. It appears that the alignment
of the bars gets shifted relative to the labels. The barchart function
cannot seem to deal with the completity of the 2 * 5 factor crossed with a
c(3,3,4) factor. On the other hand that problem seems to be present in the
original plot as well. Maybe you should re-think the structure of the data?

The problem is that levels is nested within factors:

xtabs(~levels + factors, a)

factors
levels                      Cycles MaxPairs Order
  Cycle 1                       10        0     0
  Cycle 2                       10        0     0
  Cycle 3                       10        0     0
  Cycle 4                       10        0     0
  Order 1                        0        0    10
  Order 2                        0        0    10
  Order 3                        0        0    10
  MaxPairs = 20                  0       10     0
  MaxPairs = Average Length      0       10     0
  MaxPairs = 500                 0       10     0

I can't think of a meaningful design that would give the desired result here.

-Deepayan

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