Merge branch 'viewPartition' into admix1

R/viewPartition.R

@@ -0,0 +1,121 @@
+viewPartition <- function(osuudet, popnames, COUNTS = matrix(0, 0, 0)) {
+
+    npops <- size(COUNTS, 3)
+    nind <- size(osuudet,1)
+
+# TODO: translate if necessary. Remove if this function won't be used 
+#     disp(['Number of populations: ' num2str(npops)]);
+#     if npops>30
+#         disp(' ');
+#         disp('Figure can be drawn only if the number of populations');
+#         disp('is less or equal to 30.');
+#         disp(' ');
+#         return;
+#     end
+    
+    
+#     varit = givecolors(npops);
+#     korkeinviiva = 1.05;
+#     pieninarvo = -korkeinviiva;
+    
+    
+#     h0 = figure;
+#     set(h0, 'NumberTitle', 'off'); %image_figure;   %Muutettu
+#     tiedot.popnames = popnames;
+#     tiedot.info = osuudet;
+#     set(h0,'UserData',tiedot);
+    
+#     set(gca, 'Xlim', [-.5 ,nind+.5], 'YLim', [pieninarvo ,korkeinviiva], ...
+#         'XTick', [], 'XTickLabel', [], 'YTick', [], 'YTickLabel', []);
+    
+#     for i=1:nind
+        
+#         if any(osuudet(i,:)>0)
+#             cumOsuudet = cumsum(osuudet(i,:));
+        
+#             % Pylv<6C><76>n piirt<72>minen
+#             for j=1:npops
+#                 if j==1
+#                     if cumOsuudet(1)>0
+#                         h0 =patch([i-1, i, i, i-1], [0, 0, cumOsuudet(1), cumOsuudet(1)], varit(j,:));
+#                         set(h0,'EdgeColor','none'); % Midevaa varten kommentoitava!
+#                     end
+#                 else
+#                     if (cumOsuudet(j)>cumOsuudet(j-1))
+#                         h0 = patch([i-1, i, i, i-1], [cumOsuudet(j-1), cumOsuudet(j-1), ...
+#                         cumOsuudet(j), cumOsuudet(j)], varit(j,:));
+#                         set(h0,'EdgeColor','none'); % Midevaa varten kommentoitava!
+#                     end
+#                 end
+#             end
+#         end
+#     end
+    
+    
+    
+#     if ~isempty(popnames)
+#         npops = size(popnames,1);
+#         for i=1:npops
+#             firstInd = popnames{i,2};
+#             line([firstInd-1, firstInd-1], [0,1], 'Color', 'k');  %Populaatioiden rajat
+                
+#             if i<npops
+#                 x_paikka = popnames{i,2}-1+(popnames{i+1,2}-popnames{i,2})/2;
+#             else
+#                 x_paikka = popnames{i,2}-1+(nind+1-popnames{i,2})/2;
+#             end
+                   
+#             korkeuskerroin = pieninarvo / -0.2;
+#             suhdekerroin = npops/6;
+#             for letter_num = 1:length(popnames{i,1}{1})
+#                 letter= popnames{i,1}{1}(letter_num);%alter .004|
+#                 text(x_paikka+korjaus(letter)*suhdekerroin, ...
+#                     0.0005*korkeuskerroin-0.02*letter_num*korkeuskerroin, ...
+#                     letter, 'Interpreter','none');
+#             end
+#         end
+#         line([nind,nind],[0,1],'Color','k');
+#     end
+}
+
+korjaus <- function(letter) {
+    if (any(letter %in% c('i', 'j', 'l', 'I'))) {
+            extra <- 0.022
+    } else if (any(letter == 'r')) {
+            extra <- 0.016
+    } else if (any(letter == 'k')) {
+            extra <- 0.009
+    } else if (any(letter == 'f')) {
+            extra <- 0.013
+    } else if (any(letter == 't')) {
+            extra <- 0.014
+    } else if (any(letter == 'w')) {
+            extra <- -0.003
+    } else {
+            extra <- 0
+    }
+    return(extra)
+}
+
+giveColors <- function(n) {
+        if (n > 36) stop('Maximum number of colors 36')
+        colors <- matrix(
+                data = c(
+                        1, 0, 0, 0, 1, 0, 0, 0, 1, 1, 1, 0, 1, 0, 1, 0, 1, 1,
+                        0.4, 0, 0, 0, 0.4, 0, 0, 0, 0.4, 0.4, 0.4, 0, 0.4, 0,
+                        0.4, 0, 0.4, 0.4, 0.2, 0, 0, 0, 0.2, 0, 0, 0, 0.2, 0.2,
+                        0.2, 0, 0.2, 0, 0.2, 0, 0.2, 0.2, 0.8, 0, 0, 0, 0.8, 0,
+                        0, 0, 0.8, 0.8, 0.8, 0, 0.8, 0, 0.8, 0, 0.8, 0.8, 
+                        0.6, 0, 0, 0, 0.6, 0, 0, 0, 0.6, 0.6, 0.6, 0, 0.6, 0,
+                        0.6, 0, 0.6, 0.6, 0.6, 0.2, 0.4, 0.2, 0.4, 0.8, 0.8,
+                        0.4, 0.2, 0, 0.6, 0.2, 0.2, 0.8, 0.6, 0.5, 0.2, 0.1,
+                        0.6, 0.3, 0.1
+                ),
+                ncol = 3,
+                byrow = TRUE
+        )
+        colors = colors[1:n, ]
+        # red; green; blue; yellow
+        # RGB format: [red green blue]
+        return(colors)
+}