revision2updates

code/matlab/Irish_Tuna.m

@@ -57,8 +57,7 @@
 
 %% Figure 1
 
-run figure_1a
-run figure_1b
+run figure_1
 
 %% Figure 2
 
@@ -80,21 +79,25 @@
 
 run figure_6
 
-%% Figure 7 and Table 4
+%% Figure 7 and 8
 
-run figure_7_and_table_4
+run figure_7_and_8
+
+%% Figure 9 and Table 4
+
+run figure_9_and_table_4
 
 %% Table S9 to S16
 
 run table_S9_to_S16
 
-%% Figure 8
+%% Figure 10
 
-run figure_8
+run figure_10
 
-%% Figure 9
+%% Figure 11
 
-run figure_9
+run figure_11
 
 %% Table 3 and Table S7 and S8
 
@@ -116,10 +119,6 @@
 
 run figure_S3
 
-%% Figure S4 to S6
-
-run figure_S4_to_S6
-
-%% Figure S7 to S11
+%% Figure S4
 
-run figure_S7_to_S11
+run figure_S4

code/matlab/sub_functions/figures/figure_1b.m → code/matlab/sub_functions/figures/figure_1.m

@@ -34,19 +34,14 @@
 %% Plot ocean regions.
 
 m_line(regions.NB.bndry(1,:),regions.NB.bndry(2,:),'linewi',2,'color','k');
-%m_text(-53,51.5,'Newfoundland Basin','FontWeight','bold');
 
 m_line(regions.CI.bndry(1,:),regions.CI.bndry(2,:),'linewi',2,'color','k');
-%m_text(-20.5,61.2,'Coastal Ireland','FontWeight','bold');
 
 m_line(regions.Biscay.bndry(1,:),regions.Biscay.bndry(2,:),'linewi',2,'color','k');
-%m_text(-2,51,'Bay of Biscay','FontWeight','bold');
 
 m_line(regions.WEB.bndry(1,:),regions.WEB.bndry(2,:),'linewi',2,'color','k');
-%m_text(-2,51,'West European Basin','FontWeight','bold');
 
 m_line(regions.Med.bndry(1,:),regions.Med.bndry(2,:),'linewi',2,'color','k');
-%m_text(-4.5,32,'Mediterranean','FontWeight','bold');
 
 %% Create figure border.
 
@@ -69,13 +64,12 @@
 
 set(gca,'Position',p);
 
-clear cmap
 clear p
 
 %% Save
 
 cd([fdir 'figures']);
-exportgraphics(gcf,'figure_1b.png','Resolution',300)
+exportgraphics(gcf,'figure_1.png','Resolution',300)
 
 %% Clear
 

code/matlab/sub_functions/figures/figure_8.m → code/matlab/sub_functions/figures/figure_10.m

@@ -1,4 +1,4 @@
-%% figure_8
+%% figure_10
 % Sub-function of Irish_Tuna.m; plots zoomed in bin map, ADT
 % and EKE in Newfoundland Basin hotspot
 

code/matlab/sub_functions/figures/figure_9.m → code/matlab/sub_functions/figures/figure_11.m

@@ -1,4 +1,4 @@
-%% figure_9
+%% figure_11
 % Sub-function of Irish_Tuna.m; plot ADT and EKE for WEB, CI, BoB and Med.
 
 %% West European Basin - ADT

code/matlab/sub_functions/figures/figure_2.m

@@ -1,6 +1,5 @@
 %% figure_2.m
-% Sub-function of Irish_Tuna.m; plots SSM tracks of all tags in each season
-% colored by month.
+% Sub-function of Irish_Tuna.m; plots bin map of all tags in each season.
 
 %% Loop through each season
 
@@ -15,14 +14,15 @@
     LATLIMS = [20 70]; LONLIMS = [-80 40];
     m_proj('miller','lon',LONLIMS,'lat',LATLIMS);
 
-    %% Plot bathymetry.
+    %% Bin SSM Positions
 
-    [cs,ch] = m_etopo2('contourf',-8000:500:0,'edgecolor','none');
+    binned.LONedges = -80:1:40;
+    binned.LATedges = 20:1:70;
 
-    h1 = m_contfbar([.3 .7],.05,cs,ch,'endpiece','no','FontSize',16);
-    xlabel(h1,'Bottom Depth (m)');
+    [binned.N,binned.LONmid,binned.LATmid] = twodhist(META.Longitude(META.Season == i),META.Latitude(META.Season == i),...
+        binned.LONedges,binned.LATedges);
 
-    colormap(m_colmap('blue'));
+    m_pcolor(binned.LONmid-0.25,binned.LATmid-0.25,binned.N);
 
     hold on
 
@@ -32,78 +32,21 @@
 
     hold on
 
-    %% Set colormap by month.
-
-    MM = unique(month(META.Date));
-    %cmap = getPyPlot_cMap('Paired',12);
-    cmap = [0.122,0.122,1; 0,0.773,1; 0.149,0.451,0; 0.298,0.902,0;...
-        0.914,1,0.745; 1,1,0; 1,0.666,0; 1,0,0; 0.659,0,0; 0.8,0.745,0.639;...
-        0.663,0,0.902; 1,1,1];
-    cmap_v2 = [0.122,0.122,1; 0,0.773,1; 0.149,0.451,0; 0.298,0.902,0;...
-        0.914,1,0.745; 0.9843,0.6039,0.6000; 1,0,0; 0.659,0,0;  0.9365,0.4000,0.0681; 1,0.666,0; 0.9943,0.8627,0.7294;...
-        0.6510,0.8078,0.8902];
-
-    %% Plot SSM positions of tuna colored by month.
-
-    % Plot each tag.
-    for j = 1:length(MM)
-        if i == 1 && (j == 12 || j == 1 || j == 2)
-            m(j) = m_plot(META.Longitude(MM(j) == month(META.Date)),...
-                META.Latitude(MM(j) == month(META.Date)),...
-                'ko','MarkerFaceColor',cmap_v2(j,:),'MarkerEdgeColor','k','MarkerSize',3);
-            hold on
-        else
-            m(j) = m_plot(-100,100,'o','MarkerFaceColor',cmap_v2(j,:),'MarkerEdgeColor','k','MarkerSize',3);
-        end
-        if i == 2 && (j == 3 || j == 4 || j == 5)
-            m(j) = m_plot(META.Longitude(MM(j) == month(META.Date)),...
-                META.Latitude(MM(j) == month(META.Date)),...
-                'ko','MarkerFaceColor',cmap_v2(j,:),'MarkerEdgeColor','k','MarkerSize',3);
-            hold on
-        else
-            m(j) = m_plot(-100,100,'o','MarkerFaceColor',cmap_v2(j,:),'MarkerEdgeColor','k','MarkerSize',3);
-        end
-
-        if i == 3 && (j == 6 || j == 7 || j == 8)
-            m(j) = m_plot(META.Longitude(MM(j) == month(META.Date)),...
-                META.Latitude(MM(j) == month(META.Date)),...
-                'ko','MarkerFaceColor',cmap_v2(j,:),'MarkerSize',3,'MarkerEdgeColor','k');
-            hold on
-        else
-            m(j) = m_plot(-100,100,'o','MarkerFaceColor',cmap_v2(j,:),'MarkerEdgeColor','k','MarkerSize',3);
-        end
-
-        if i == 4 && (j == 9 || j == 10 || j == 11)
-            m(j) = m_plot(META.Longitude(MM(j) == month(META.Date)),...
-                META.Latitude(MM(j) == month(META.Date)),...
-                'ko','MarkerFaceColor',cmap_v2(j,:),'MarkerSize',3,'MarkerEdgeColor','k');
-            hold on
-        else
-            m(j) = m_plot(-100,100,'o','MarkerFaceColor',cmap_v2(j,:),'MarkerEdgeColor','k','MarkerSize',3);
-        end
-    end
-    clear j
-
     %% Plot ICCAT regions.
 
     m_line([-45 -45],[20 70],'linewi',2,'color','k','linestyle','--')
 
     %% Plot ocean regions.
 
     m_line(regions.NB.bndry(1,:),regions.NB.bndry(2,:),'linewi',2,'color','k');
-    %m_text(-53,51.5,'Newfoundland Basin','FontWeight','bold');
 
     m_line(regions.CI.bndry(1,:),regions.CI.bndry(2,:),'linewi',2,'color','k');
-    %m_text(-20.5,61.2,'Coastal Ireland','FontWeight','bold');
 
     m_line(regions.Biscay.bndry(1,:),regions.Biscay.bndry(2,:),'linewi',2,'color','k');
-    %m_text(-2,51,'Bay of Biscay','FontWeight','bold');
 
     m_line(regions.WEB.bndry(1,:),regions.WEB.bndry(2,:),'linewi',2,'color','k');
-    %m_text(-2,51,'West European Basin','FontWeight','bold');
 
     m_line(regions.Med.bndry(1,:),regions.Med.bndry(2,:),'linewi',2,'color','k');
-    %m_text(-4.5,32,'Mediterranean','FontWeight','bold');
 
     %% Create figure border.
 
@@ -126,13 +69,19 @@
         title('Fall','FontSize',26);
     end
 
-    %% Add Legend
+    %% Add colorbar
+
+    % p = get(gca,'Position');
+
+    % h = colorbar('FontSize',16);
+    colormap(flipud(hot(1500)));
+    % ylabel(h,'Number of Daily Geolocations','FontSize',16);
+    caxis([0 50]);
+    % h.Ticks = 0:10:50;
+
+    % set(gca,'Position',p);
 
-%     [~,icon] = legend(m,{'Jan','Feb','Mar','Apr','May','Jun','Jul','Aug','Sep','Oct','Nov','Dec'},'FontSize',14,'Location','bestoutside');
-%     icons = findobj(icon, 'type', 'line');
-%     set(icons,'MarkerSize',12);
-%     clear MM
-%     clear icon*
+    % clear p
 
     %% Save figure.
 
@@ -141,7 +90,7 @@
 
     %% Clear
 
-    clear ax* c* h* m M *LIMS
+    clear ax* c* h* *LIMS
     clear ans
 
     close gcf
@@ -150,4 +99,3 @@
 
 clear i
 clear tmp
-clear MM

code/matlab/sub_functions/figures/figure_S4_to_S6.m → code/matlab/sub_functions/figures/figure_7_and_8.m

@@ -1,17 +1,16 @@
-%% figure_S3_to_S5
+%% figure_7_and_8
 % Sub-function of Irish_Tuna.m; plots timeseries and track for 3 tags. Need
 % to manually edit filename each time.
 
 %% Define filename.
 
 % 5116034
 % 5116043
-% 5120057
 
 cd([fdir 'data/archival']);
 
-% filename = '5116034_14P0031_clean.csv';
-filename = '5116043_16P1265_clean.csv';
+filename = '5116034_14P0031_clean.csv';
+% filename = '5116043_16P1265_clean.csv';
 % filename = '5120057_L330-2973_clean.csv';
 
 %% Load PAT data.
@@ -143,9 +142,12 @@
 hold on
 
 MM = unique(month(META.Date));
-cmap = [0.122,0.122,1; 0,0.773,1; 0.149,0.451,0; 0.298,0.902,0;...
-        0.914,1,0.745; 0.9843,0.6039,0.6000; 1,0,0; 0.659,0,0;  0.9365,0.4000,0.0681; 1,0.666,0; 0.9943,0.8627,0.7294;...
-        0.6510,0.8078,0.8902];
+cmap = [0.122,0.122,1 ; 0,0.773,1; 0.149,0.451,0; 0.298,0.902,0;...
+        0.914,1,0.745; 1,1,0; 1,0.666,0; 1,0,0; 0.659,0,0; 0.8,0.745,0.639;...
+        0.663,0,0.902; 1,1,1];
+% cmap = [0.122,0.122,1; 0,0.773,1; 0.149,0.451,0; 0.298,0.902,0;...
+%         0.914,1,0.745; 0.9843,0.6039,0.6000; 1,0,0; 0.659,0,0;  0.9365,0.4000,0.0681; 1,0.666,0; 0.9943,0.8627,0.7294;...
+%         0.6510,0.8078,0.8902];
 
 tmp.lon = META.Longitude(META.TOPPid == str2double(filename(1:7)));
 tmp.lat = META.Latitude(META.TOPPid == str2double(filename(1:7)));
@@ -160,12 +162,12 @@
 
 for j = 1:length(MM)
     if isempty(tmp.lon(MM(j) == month(tmp.date)))
-        m(j) = m_plot(-100,100,'o','MarkerFaceColor',cmap(j,:),'MarkerEdgeColor','k','MarkerSize',5);
+        m(j) = m_plot(-100,100,'o','MarkerFaceColor',cmap(j,:),'MarkerEdgeColor','k','MarkerSize',6);
         hold on
     else
         m(j) = m_plot(tmp.lon(MM(j) == month(tmp.date)),...
             tmp.lat(MM(j) == month(tmp.date)),...
-            'ko','MarkerFaceColor',cmap(j,:),'MarkerEdgeColor','k','MarkerSize',5);
+            'ko','MarkerFaceColor',cmap(j,:),'MarkerEdgeColor','k','MarkerSize',6);
         hold on
     end
 end
@@ -178,16 +180,16 @@
 m_line(regions.WEB.bndry(1,:),regions.WEB.bndry(2,:),'linewi',2,'color','k');
 m_line(regions.Med.bndry(1,:),regions.Med.bndry(2,:),'linewi',2,'color','k');
 
-m_grid('linewi',2,'tickdir','in','linest','none','fontsize',24);
+m_grid('linewi',2,'tickdir','in','linest','none','fontsize',20);
 
 m_northarrow(-75,65,4,'type',2,'linewi',2);
 m_ruler([.78 .98],.1,2,'fontsize',16,'ticklength',0.01);
 
 cd([fdir 'figures']);
 if str2double(filename(1:7)) == 5116034
-    exportgraphics(gcf,'figure_S4b.png','Resolution',300);
+    exportgraphics(gcf,'figure_7b.png','Resolution',300);
 elseif str2double(filename(1:7)) == 5116043
-    exportgraphics(gcf,'figure_S5b.png','Resolution',300);
+    exportgraphics(gcf,'figure_8b.png','Resolution',300);
 elseif str2double(filename(1:7)) == 5120057
     exportgraphics(gcf,'figure_S6b.png','Resolution',300);
 end

code/matlab/sub_functions/figures/figure_7_and_table_4.m → code/matlab/sub_functions/figures/figure_9_and_table_4.m

@@ -1,4 +1,4 @@
-%% figure_7_and_table_4.m
+%% figure_9_and_table_4.m
 % Sub-function of Irish_Tuna.m; plots eddy histograms with each region and
 % compute eddy statistics.