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POHow to set the display bounds of a raster::plot?
 

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  1. POHow to set the display bounds of a raster::plot?
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    <h1>summary</h1> <p>How to limit display of an R <code>raster::plot</code> to the bounds of a Raster* object? Why I ask:</p> <p>I'm an R beginner who must</p> <ol> <li>convert unprojected (lon-lat) global spatial data from ASCII to <a href="http://en.wikipedia.org/wiki/Netcdf" rel="nofollow noreferrer">netCDF</a> (solved)</li> <li>"regrid" it: i.e., restricted the data to a region, project it, and downscale (decrease the size of the gridcells) it (mostly solved)</li> </ol> <p>Unfortunately, in scientific work, one mostly QAs data transformations such as this by visual inspection. Step 1 above looks good. But though step 2 now looks much better, I really want to plot <strong>only</strong> the bounds (or <code>extents</code>) of the regridded <code>RasterLayer</code>. I have R code driven by bash scripts in a public git repository (<a href="https://github.com/TomRoche/GEIA_to_netCDF" rel="nofollow noreferrer">here</a>) that does the conversion step, and plots the converted output, <a href="https://i.stack.imgur.com/SOmvZ.png" rel="nofollow noreferrer">apparently correctly</a>. However my attempts to plot the output of the regridding with <code>raster::plot</code> are not quite right (see first 3 pages of output <a href="https://github.com/downloads/TomRoche/GEIA_to_netCDF/GEIA_N2O_oceanic_regrid.pdf" rel="nofollow noreferrer">here</a>).</p> <p>How to fix?</p> <h1>details</h1> <h2>background</h2> <p>I need to take some data (a global marine emissions inventory (EI)), combine it with other data (mostly other EIs), and input that to a model. The model wants to consume netCDF, and it wants that netCDF over a spatial domain slightly bigger than the contiguous US (CONUS). The borders of this image <img src="https://github.com/TomRoche/cornbeltN2O/wiki/images/Cmaq_aqmeii_domain.png" alt="AQMEII-NA domain"> are the boundaries of the domain. (Note that part, but only part, of the domain is oceanic.) The model also wants that netCDF projected a certain way (<a href="http://en.wikipedia.org/wiki/Lambert_conformal_conic" rel="nofollow noreferrer">LCC</a> at 12-km resolution). I'm treating this as 2 independent problems:</p> <ol> <li>convert the global EI from its native ASCII format to netCDF</li> <li>"regrid" the netCDF from global/unprojected to the downscaled (finer-resolution), projected subdomain.</li> </ol> <p>I'm attempting to solve these problems with code I have archived at <a href="https://github.com/TomRoche/GEIA_to_NetCDF" rel="nofollow noreferrer">this public git repository</a>. If you clone that git repo, and then configure/run the bash driver <code>GEIA_to_netCDF.sh</code> as described for the "first example" <a href="https://github.com/TomRoche/GEIA_to_netCDF/blob/master/README.md" rel="nofollow noreferrer">in the README</a> (and presuming your R is appropriately configured, notably with packages=<code>raster</code>, <code>ncdf4</code>) it will output netCDF and plot (using <code>fields::image.plot</code>) that output to a <a href="https://github.com/downloads/TomRoche/GEIA_to_netCDF/GEIA_N2O_oceanic.pdf" rel="nofollow noreferrer">PDF</a>, which should look like this: <img src="https://github.com/downloads/TomRoche/GEIA_to_netCDF/GEIA_N2O_oceanic.png" alt="GEIA global marine emissions">. The distribution of the output data appears correct, so problem 1 seems solved.</p> <h2>problem</h2> <p>Solving problem 2 (aka the "second example" <a href="https://github.com/TomRoche/GEIA_to_netCDF/blob/master/README.md" rel="nofollow noreferrer">in the README</a>) seems to require R package=<code>raster</code>. My bash driver <a href="https://github.com/TomRoche/GEIA_to_netCDF/blob/master/regrid_GEIA_netCDF.sh" rel="nofollow noreferrer"><code>regrid_GEIA_netCDF.sh</code></a> calls <a href="https://github.com/TomRoche/GEIA_to_netCDF/blob/master/regrid.global.to.AQMEII.r" rel="nofollow noreferrer"><code>regrid.global.to.AQMEII.r</code></a> (both <a href="https://github.com/TomRoche/GEIA_to_NetCDF" rel="nofollow noreferrer">in repository</a>), which runs without error, and displays a PDF of its output. <a href="https://github.com/downloads/TomRoche/GEIA_to_netCDF/GEIA_N2O_oceanic_regrid.pdf" rel="nofollow noreferrer"><code>GEIA_N2O_oceanic_regrid.pdf</code></a> comprises 4 pages, corresponding to 4 blocks of code at the end of <code>regrid.global.to.AQMEII.r</code>. Only the first 3 pages are relevant here (the 4th page tries to use <code>fields::image.plot</code> and has bigger problems).</p> <p>Page=1/4 results from a simple <code>raster::plot</code> of the regridded output, plus a projected version of a CONUS map from <code>wrld_simpl</code>:</p> <pre><code>plot(out.raster) plot(map.us.proj, add=TRUE) </code></pre> <p>Unfortunately the output appears global, or nearly so: <img src="https://i.stack.imgur.com/XLIZk.png" alt="raster::plot bounds problem"> But the desired domain, to which the output was regridded, is much smaller: <img src="https://github.com/TomRoche/cornbeltN2O/wiki/images/Cmaq_aqmeii_domain.png" alt="AQMEII-NA domain">. So I have 3 questions (1 main question, 2 followups):</p> <ol> <li>Does the image displayed by <code>raster::plot</code> by default display <em>only</em> the extents of the <code>RasterLayer</code> given in its arguments?</li> <li>If so, what is wrong with my regrid? (more below)</li> <li>If not (i.e., if <code>raster::plot</code> by default displays <em>more</em> than the extents of its <code>RasterLayer</code>), how to make <code>raster::plot</code> display only the extents of that <code>RasterLayer</code>?</li> </ol> <p>The code in <code>regrid.global.to.AQMEII.r</code> (<a href="https://github.com/TomRoche/GEIA_to_netCDF/blob/master/regrid.global.to.AQMEII.r" rel="nofollow noreferrer">here</a>) that does the regridding seems to get the correct output:</p> <pre><code>out.crs &lt;- '+proj=lcc +lat_1=33 +lat_2=45 +lat_0=40 +lon_0=-97 +x_0=-2556000 +y_0=-1728000' </code></pre> <p>Note that CRS appears to match the definition of the output domain given <a href="https://github.com/TomRoche/cornbeltN2O/wiki/AQMEII-North-American-domain#wiki-EPA" rel="nofollow noreferrer">here</a>. (Once at the linked page, scroll past the map.)</p> <pre><code>out.raster &lt;- projectRaster( from=in.raster, to=template.raster, method='bilinear', crs=out.crs, overwrite=TRUE, progress='window', format='CDF', # args from writeRaster NAflag=-999.0, # match emi_n2o:missing_value,_FillValue (TODO: copy) varname=data.var.name, varunit='ton N2O-N/yr', longname='N2O emissions', xname='COL', yname='ROW', filename=out.fp) out.raster # made with CRS #&gt; class : RasterLayer #&gt; dimensions : 299, 459, 137241 (nrow, ncol, ncell) #&gt; resolution : 53369.55, 56883.69 (x, y) #&gt; extent : -14802449, 9694173, -6258782, 10749443 (xmin, xmax, ymin, ymax) # ??? why still proj=longlat ??? #&gt; coord. ref. : +proj=longlat +datum=WGS84 +ellps=WGS84 +towgs84=0,0,0 #&gt; data source : /home/rtd/code/R/GEIA_to_netCDF/GEIA_N2O_oceanic_regrid.nc #&gt; names : N2O.emissions #&gt; zvar : emi_n2o </code></pre> <p>But, as noted, the regrid output (<code>out.raster</code>) shows itself to be lon-lat in its CRS: I'm not sure why that is, or if it implies <code>out.raster</code> is global in extents.</p> <p>I also tried to restrict the plot itself in two ways:</p> <p>Firstly, I tried adding an <code>extents</code> to the plot, i.e.,</p> <pre><code>plot(out.raster, ext=template.raster) plot(map.us.proj, add=TRUE) </code></pre> <p>which generates page=2/4 of <a href="https://github.com/downloads/TomRoche/GEIA_to_netCDF/GEIA_N2O_oceanic_regrid.pdf" rel="nofollow noreferrer">the PDF</a>. Unfortunately, that does not change the output at all: AFAICS, it is completely identical to page=1/4 (above).</p> <p>Secondly, I tried using <code>raster::crop</code> to bound the regridded netCDF itself, before plotting that, using the same <code>RasterLayer</code> object (<code>template.raster</code>) that I used to bound the regrid:</p> <pre><code>template.raster.extent &lt;- extent(template.raster) out.raster.crop &lt;- # overwrite the uncropped file crop(out.raster, template.raster.extent, filename=out.fp, overwrite=TRUE) ... plot(out.raster.crop) plot(map.us.proj, add=TRUE) </code></pre> <p>which generates page=3/4 of <a href="https://github.com/downloads/TomRoche/GEIA_to_netCDF/GEIA_N2O_oceanic_regrid.pdf" rel="nofollow noreferrer">the PDF</a>. Unfortunately, that it is also apparently completely identical to page=1/4 (above).</p> <p>(In case you're wondering, page 4 of the PDF was generated using <code>fields::image.plot</code>, which has a different problem, described <a href="https://stackoverflow.com/questions/13022919/r-problems-visualizing-a-raster-with-fieldsimage-plot">here</a>, unless StackOverflow whacks that link.)</p> <p>Your assistance to this R newbie is appreciated!</p>
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