[R] Plotting question

[Bert Gunter]

Well stated, Duncan, and I plead guilty, though I did try to weasel
out with caveats.

Perhaps I may plead down to a lesser sentence or probation by saying
that I was offering what I still believe to be appropriate advice for
a general strategy for handling this sort of plotting issue; but that
as always, one's mileage may vary depending on the specifics.

Extra inline comments below.

Cheers,
Bert

And to return to R, note that any of these options is easy to
implement in any of at least 3 different graphics frameworks (base,
trellis, and ggplot). So Duncan and I can spar over what we'd like to
do without being limited by what software **allows** us to do.


On Mon, Aug 1, 2011 at 1:48 PM, Duncan Murdoch <murdoch.duncan at gmail.com> wrote:
> On 11-08-01 11:48 AM, Bert Gunter wrote:
>>
>> IMHO:
>>
>> On Mon, Aug 1, 2011 at 7:51 AM, Duncan Murdoch<murdoch.duncan at gmail.com>
>>  wrote:
>>>
>>> On 11-08-01 5:44 AM, Andrew McCulloch wrote:
>>>>
>>>> Hi,
>>>>
>>>> I use R to draw my graphs. I have 100 points on a simple xy-plot. The
>>>> points are
>>>> distinguished by a third variable which is categorical with 10 levels. I
>>>> have
>>>> been plotting x against y and using gray scales to distinguish the level
>>>> of the
>>>> categorical variable for each point. It looks ok to me but a journal
>>>> reviewer
>>>> says this is not any use. I cannot afford to pay for colour prints. Any
>>>> ideas on
>>>> what is the best way to distinguish 10 groups on an xy scatter plot?
>>>
>>> Plot digits or letters or other symbols.
>>>
>>> Duncan Murdoch
>>>
>> No, this does not work.
>
> You have amazing perception to know that it doesn't work in Andrew's graph.
>  But then you go on to suggest that sometimes it does, and then suggest
> using symbols.
>
> Obviously you need to see the graph to know what works.  If the 10
> categories are ordered, then something like thermometer plots would work.
>  If they are grouped into a small number of variations on a small number of
> groups, then digits or letters combined with shading might work, especially
> if the groups are well separated, or there are clear patterns.
>
> I'd agree with the reviewer than 10 levels of shading is probably too many
> to distinguish,

But for ordered categories you may not wish to distinguish so much as
give an overall gestalt, for which a gray scale with 10 levels could
work quite well. So it depends on the specifics of what's being
plotted, no?

and I'd agree with you that digits 0-9 in equal quantities
> in an unstructured scatterplot are probably not a good presentation, but I
> wouldn't want to give specific advice about plotting a dataset without
> seeing it.
>
> Duncan Murdoch
>
> See Cleveland's books (e.g. "Visualizing
>>
>> Data"). 10 is too many symbols to constantly refer to a legend to keep
>> straight, and digits or letters do not allow you to readily perceive
>> the pattern. (Caveat: If "most" of the data are only 2 or 3 of the
>> symbols, then these can work).
>>
>> I think the OP's idea of using gray scales was better. I would dispute
>> the reviewer and refer them to appropriate references. Alternatively,
>> thermometer plots (aka "filled rectangle" plots) would be best. Again,
>> Cleveland's books provide scientific justification rather than merely
>> the (possibly uninformed) aesthetic opinion of a reviewer. Presumably,
>> the journal editor would accept hard data and psychological research
>> in preference to opinions.
>>
>>>>
>>>>
>>>>
>>>> If all else fails I can just remove the graph and give them a table of
>>>> regression coefficients.
>>
>> No. I think your attempt to use a graph is a much better way to go.
>> Try to resist poor practices such as just publishing summary
>> statistics.
>>
>> Cheers,
>> Bert
>>>>
>>>>
>>>> Thanks.
>>>>
>>>> Yours Sincerely
>>>> Andrew McCulloch
>>>>
>>>> ______________________________________________
>>>> R-help at r-project.org mailing list
>>>> https://stat.ethz.ch/mailman/listinfo/r-help
>>>> PLEASE do read the posting guide
>>>> http://www.R-project.org/posting-guide.html
>>>> and provide commented, minimal, self-contained, reproducible code.
>>>
>>> ______________________________________________
>>> R-help at r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/r-help
>>> PLEASE do read the posting guide
>>> http://www.R-project.org/posting-guide.html
>>> and provide commented, minimal, self-contained, reproducible code.
>>>
>>
>>
>>
>
>



-- 
"Men by nature long to get on to the ultimate truths, and will often
be impatient with elementary studies or fight shy of them. If it were
possible to reach the ultimate truths without the elementary studies
usually prefixed to them, these would not be preparatory studies but
superfluous diversions."

-- Maimonides (1135-1204)

Bert Gunter
Genentech Nonclinical Biostatistics