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.biv...@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. > > ______________________________________________ > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see > 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. -- Regards, Preethi Malur Balaji | PhD Student University College Cork | Cork, Ireland. ______________________________________________ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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.