Plot composite charts (issue #7)

Makefile

@@ -59,20 +59,31 @@ findability_level_2: data/findability-wcvp-map-level-2.png
 findability_level_3: data/findability-wcvp-map-level-3.png
 findability_all: data/findability-wcvp-map-level-1.png data/findability-wcvp-map-level-2.png data/findability-wcvp-map-level-3.png
 
+# Map WCVP data: composites
+data/wcvp-map-composite-level-%.png: plotoageo.py data/ipniname-oastatus-wcvp-report-%.csv downloads/level%.geojson
+	$(python_launch_cmd) $^ $(limit_args) --tdwg_wgsrpd_level=$* --plot-maps --plot-composite --outputfile-composite=$@ data/oaratio-wcvp-map-level-$*.png data/findability-wcvp-map-level-$*.png
+# Shorthand:
+composite_level_1: data/wcvp-map-composite-level-1.png
+composite_level_2: data/wcvp-map-composite-level-2.png
+composite_level_3: data/wcvp-map-composite-level-3.png
+composite_all: data/wcvp-map-composite-level-1.png data/wcvp-map-composite-level-2.png data/wcvp-map-composite-level-3.png
+
 ###############################################################################
 
 oatrends_charts_year:=data/ipni-oatrend-year.png
 oastatus_charts_year:= data/ipni-oastatustrendpc.png
 oatrends_charts_publ:=data/ipni-oatrend-publ.png
 
 findability_charts:= data/findability-wcvp-map-level-1.png data/findability-wcvp-map-level-2.png data/findability-wcvp-map-level-3.png
+composite_charts:=data/wcvp-map-composite-level-1.png data/wcvp-map-composite-level-2.png data/wcvp-map-composite-level-3.png 
+
 oa_charts: data/oaratio-wcvp-map-level-1.png data/oaratio-wcvp-map-level-2.png data/oaratio-wcvp-map-level-3.png
 
-all: $(findability_charts) $(oaratio_charts)
+all: $(findability_charts) $(oaratio_charts) $(composite_charts)
 
 data_archive_zip:=$(shell basename $(CURDIR))-data.zip
 
-archive: $(findability_charts) $(oaratio_charts)
+archive: $(findability_charts) $(oaratio_charts) $(composite_charts)
 	mkdir -p archive	
 	echo "Archived on $(date_formatted)" >> data/archive-info.txt
 	zip archive/$(data_archive_zip) data/archive-info.txt data/* -r

plotoageo.py

@@ -22,6 +22,8 @@ def main():
     parser.add_argument("--tdwg_wgsrpd_level", default=2, type=int)
     parser.add_argument("--tax_novs_only", action='store_true')
     parser.add_argument('--plot-maps', action='store_true')
+    parser.add_argument('--plot-composite', action='store_true')
+    parser.add_argument('--outputfile_composite', default=None)
     parser.add_argument('-d','--delimiter', type=str, default='\t')
     parser.add_argument('--year_min',default=2012)
     parser.add_argument('--year_max',default=2021)
@@ -99,5 +101,27 @@ def main():
     fig.tight_layout(pad=0)
     plt.savefig(args.outputfile_unknown, bbox_inches='tight',pad_inches = 0.1, dpi = 400)
 
+    # 3.3 plot composite if required
+    if args.plot_composite:
+        fig, ax = plt.subplots(2, 1)
+        # Repeat of above - TODO extract to reusable method
+        world.plot(column='OA_unfind',ax=ax[0], legend=True, legend_kwds=dict(loc='lower left',fontsize='x-small'), cmap='OrRd', scheme='quantiles')
+        ax[0].set_title("Proportion of un-discoverable publications of {} IPNI nomenclatural acts ({}-{})".format(coverage,args.year_min,args.year_max))
+        ax[0].xaxis.set_visible(False)
+        ax[0].yaxis.set_visible(False)
+
+        # Repeat of above - TODO extract to reusable method
+        world.plot(column='OA_ratio',ax=ax[1], legend=True, legend_kwds=dict(loc='lower left',fontsize='x-small'), cmap='OrRd', scheme='quantiles')
+        coverage = 'all'
+        if args.tax_novs_only:
+            coverage = 'tax. nov.'
+        ax[1].set_title("Ratio of open:closed access of {} IPNI nomenclatural acts ({}-{})".format(coverage,args.year_min,args.year_max))
+        ax[1].xaxis.set_visible(False)
+        ax[1].yaxis.set_visible(False)
+
+        fig.tight_layout(pad=0)
+        plt.savefig(args.outputfile_composite, bbox_inches='tight',pad_inches = 0.1, dpi = 400)
+
+
 if __name__ == "__main__":
     main()