[R] Boxplot using a shapefile

[Preethi Balaji]

Dear all,

Thanks very much for your help! I will keep your suggestions in mind
and will get back to you if I get stuck!



On Tue, Jun 16, 2015 at 1:28 PM, Roger Bivand <Roger.Bivand at nhh.no> wrote:
> Boris Steipe <boris.steipe <at> utoronto.ca> writes:
>
>>
>> Your workflow in principle is:
>>
>> - read the image into an object for which you can obtain values-per-pixel
> in a 2D structure;
>> - read the shapefile and convert into a polygon;
>> - determine the bounding box of the polygon;
>> - use the inout() function of the splancs package to get a list of
> booleans for the
>>     points in the bounding box, TRUE if they are _inside_ the polygon;
>> - subset your image points to those for which inout() returns TRUE;
>> - plot as boxplot().
>>
>> The CRAN taskview http://cran.r-project.org/web/views/MedicalImaging.html
> has a section on general
>> image processing, guiding you to helpful packages.
>
> Actually, this is the wrong taskview if the data are as described, as
> Spatial data are covered in the Spatial task view at:
>
> http://cran.r-project.org/web/views/Spatial.html
>
> The workflow as described is also muddled: "[T]he shapefile takes the
> pixel values from the image and shows the distribution of pixels in
> the form of a boxplot" doesn't actually mean anything without further
> assumptions.
>
> A shapefile is an ESRI file format for GIS vector geometries (and
> attributes) that may be polygons, lines or points, and has an associated
> coordinate reference system; it is almost never used for other kinds of data.
>
> The "image" - presumably a GIS raster data file, should have the same
> coordinate reference system, or be transformed to the same system (use
> spTransform in the rgdal package, which is also the package you should use
> for reading the input data as it correctly reads input coordinate reference
> systems if available).
>
> The operation then needed is called an over() method in the sp package, and
> extract() in the raster package.
>
> If the shapefile contains points, the over query is asking the value(s) of
> the raster cells (pixels) at those points, given the same coordinate
> reference systems - but only one boxplot. If lines, for each line you may
> get a vector of values from raster cells intersected by the lines, and could
> make a boxplot for each line; you may wish to weight each value by the
> length of line in each cell. If polygons, as lines, with weighting by
> intersection area.
>
> The over vignette in the sp package is where you need to go to begin:
>
> http://cran.r-project.org/web/packages/sp/vignettes/over.pdf
>
> and the introduction to the raster package as a further reference:
>
> http://cran.r-project.org/web/packages/raster/vignettes/Raster.pdf
>
>>
>> Ask again if you get stuck - but(!):
>> - see here for some hints on how to ask questions productively:
>>   http://adv-r.had.co.nz/Reproducibility.html
>>
> http://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible-example
>> - ... and please read the posting guide and don't post in HTML.
>>
>
> Definitely! And note that this is a question that is better suited to the
> R-sig-geo list.
>
> Hope this clarifies,
>
> Roger
>
>> B.
>>
>> On Jun 15, 2015, at 7:19 AM, Preethi Balaji <preet.balaji20 <at>
> gmail.com> wrote:
>>
>> > Dear all,
>> >
>> > I am trying to generate boxplots by giving a shapefile and an image as
>> > input. The shapefile takes the pixel values from the image and shows
>> > the distribution of pixels in the form of a boxplot.
>> >
>> > Can somebody please tell me how I can execute this in R?
>> >
>> > Many thanks!
>> >
>> > --
>> >
>> > Regards,
>> > Preethi Malur Balaji | PhD Student
>> > University College Cork | Cork, Ireland.
>
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-- 

Regards,
Preethi Malur Balaji | PhD Student
University College Cork | Cork, Ireland.