I have finally solved this riddle while reading the source code of boxplot in axes.py file. And yes whisker plotting is done different than I expect. When I assigned "whis" keyword to 3.0 the lower whisker is plotted on the right spot. And Josh, yes you were right, it did plot the lower whisker as seen on my very first uploaded image.

Still a question stays in my mind: How do you decribe box-whisker plots in your writing while using matplotlib's boxplot command? It uses 25, 50, 75th percentiles of the data for sure, but apart from what I expected whiskers are not at 5th, and 95th percentiles of the data respectively.

Could someone please comment on this?


On Wed, May 13, 2009 at 8:43 PM, Gökhan SEVER <gokhansever@gmail.com> wrote:
One more point to add.

I issued one more boxplot with prctile(data) (a mlab command which boxplot calls internally to calculate percentiles) as an argument to it.

Guess what?

I get almost the same as in initially I have :) without a lower whisker.

I don't know I am confusing myself or is it the data...


On Wed, May 13, 2009 at 7:56 PM, Gökhan SEVER <gokhansever@gmail.com> wrote:

With this figure, it is clearer to see what's wrong with two of my boxplots. I pull the original data and feed boxplot with it.

The 1st boxplot is using only quartiles and the next is providing the actual data array.


To me the second boxplot seems more convenient to put an academic paper. What do you think? These boxplots only show the variation in true air speed of a small leg of a research flight.

Would there be a better representation of in addition to / as an alternative boxplotting?


On Wed, May 13, 2009 at 1:41 PM, Gökhan SEVER <gokhansever@gmail.com> wrote:
Thank you for the response once again.

That's why I am suspecting actually the raw data. At the problem points there might be not included values or missing values where not exist on the normal plots.

I will find the original data and feed boxplot with it to see how it effects the final result.


On Wed, May 13, 2009 at 12:58 PM, Josh Hemann <jhemann@vni.com> wrote:

Thanks for sending the data and code. After playing around some I still don't
have a confident guess as to the problem (or solution), but here is what I
would look at more...

I issued   plot(d[i][8:])   for i 0,1,...11  and looked at the shape of the
lines. For the two problem boxes, the plots of the associated data have
steep jumps between the 5th and 25th percentiles, when compared with the
data associated with the "good" boxes. So, what you have calculated as the
5th and 25th percentiles are not necessarily calculated by boxplot as such
because boxplot does not know that you are handing it percentiles of your
underlying data: boxplot actually computes the percentiles assuming that the
input _is_ the raw data. I would guess that if you gave boxplot the raw data
you would not see this issue of missing whiskers.
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