Merge pull request #893 from shawnlaffan/issue_820_divergent_colours

Support divergent and ratio colouring, as well as inversion of colour schemes
shawnlaffan · Dec 4, 2023 · 3de625a · 3de625a
2 parents 670c6df + 288e035
commit 3de625a
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Showing 15 changed files with 663 additions and 68 deletions.
diff --git a/.github/workflows/macos.yml b/.github/workflows/macos.yml
@@ -35,7 +35,7 @@ jobs:
           which cpanm
 
       - name: Install GDAL and its deps
-        run: brew install gdal
+        run: brew install --force --overwrite gdal
 
       - name: perl -V
         run: perl -V

diff --git a/.gitignore b/.gitignore
@@ -20,3 +20,4 @@ biodiverse.iml
 /xx.bps
 /biodiverseb.iml
 /.idea
+/AGS_bin
diff --git a/bin/ui/hboxClusteringPage.ui b/bin/ui/hboxClusteringPage.ui
@@ -222,6 +222,15 @@ Uses the min and max determined by the Colour stretch choice.</property>
                             <property name="use_underline">True</property>
                           </object>
                         </child>
+                        <child>
+                          <object class="GtkCheckMenuItem" id="menu_dendro_colour_stretch_flip_mode">
+                            <property name="visible">True</property>
+                            <property name="can_focus">False</property>
+                            <property name="tooltip_text" translatable="yes">Invert (flip) the colour range. Has no effect on categorical colouring.</property>
+                            <property name="label" translatable="yes">Invert colour stretch</property>
+                            <property name="use_underline">True</property>
+                          </object>
+                        </child>
                         <child>
                           <object class="GtkMenuItem" id="menu_item_dendro_colour_stretch">
                             <property name="visible">True</property>

diff --git a/bin/ui/hboxSpatialPage.ui b/bin/ui/hboxSpatialPage.ui
@@ -222,6 +222,15 @@
                             <property name="use_underline">True</property>
                           </object>
                         </child>
+                        <child>
+                          <object class="GtkCheckMenuItem" id="menu_colour_stretch_flip_mode">
+                            <property name="visible">True</property>
+                            <property name="can_focus">False</property>
+                            <property name="tooltip_text" translatable="yes">Invert (flip) the colour range. Has no effect on categorical colouring.</property>
+                            <property name="label" translatable="yes">Invert colour stretch</property>
+                            <property name="use_underline">True</property>
+                          </object>
+                        </child>
                         <child>
                           <object class="GtkMenuItem" id="menu_item_colour_stretch">
                             <property name="visible">True</property>
@@ -490,10 +499,22 @@ Colours are scaled using percentiles defined in the colour stretch menu. </prope
                             <property name="visible">True</property>
                             <property name="can_focus">False</property>
                             <property name="label" translatable="yes">Log scale</property>
+                            <property name="tooltip_text" translatable="yes">Log scale the colours.
+Uses the min and max determined by the Colour stretch choice.</property>
                             <property name="use_underline">True</property>
                             <property name="active">True</property>
                           </object>
                         </child>
+                        <child>
+                          <object class="GtkCheckMenuItem" id="menuitem_spatial_tree_colour_stretch_flip_mode">
+                            <property name="visible">True</property>
+                            <property name="can_focus">False</property>
+                            <property name="label" translatable="yes">Invert colour stretch</property>
+                            <property name="tooltip_text" translatable="yes">Invert (flip) the colour range. Has no effect on categorical colouring.</property>
+                            <property name="use_underline">True</property>
+                            <property name="active">False</property>
+                          </object>
+                        </child>
                         <child>
                           <object class="GtkMenuItem" id="menuitem_spatial_tree_colour_mode">
                             <property name="visible">True</property>

diff --git a/lib/Biodiverse/GUI/Dendrogram.pm b/lib/Biodiverse/GUI/Dendrogram.pm
@@ -871,12 +871,19 @@ sub recolour_cluster_elements {
 
     my $cluster_colour_mode = $self->get_cluster_colour_mode();
     my $colour_callback;
-
+
+    my %list_and_index = (list => $list_name, index => $list_index);
     my $is_canape = $list_name =~ />>CANAPE>>/ && $list_index =~ /CANAPE/;
     my $is_zscore = eval {
-        $parent_tab->index_is_zscore(list => $list_name, index => $list_index);
+        $parent_tab->index_is_zscore(%list_and_index);
     };
     my $is_prank = $list_name =~ />>p_rank>>/;
+    my $is_ratio
+        = !$is_prank && !$is_zscore
+        && eval {$parent_tab->index_is_ratio(%list_and_index)};
+    my $is_divergent
+        = !$is_prank && !$is_zscore && !$is_ratio
+        && eval {$parent_tab->index_is_divergent(%list_and_index)};
 
     if ($cluster_colour_mode eq 'palette') {
         # sets colours according to palette
@@ -917,6 +924,18 @@ sub recolour_cluster_elements {
         };
     }
     elsif ($cluster_colour_mode eq 'list-values') {
+        my $abs_extreme;
+        if ($is_ratio) {
+            $abs_extreme = exp (max (abs log $analysis_min, log $analysis_max));
+            $analysis_min = 1 / $abs_extreme;
+            $analysis_max = $abs_extreme;
+        }
+        elsif ($is_divergent) {  #  assumes zero - needs work
+            $abs_extreme = max(abs $analysis_min, abs $analysis_max);
+            $analysis_min = 0;
+            $analysis_max = $abs_extreme;
+        }
+
         # sets colours according to (usually spatial)
         # list value for the element's cluster
         $colour_callback = sub {
@@ -936,6 +955,8 @@ sub recolour_cluster_elements {
                 return $is_canape ? $map->get_colour_canape ($val)
                      : $is_zscore ? $map->get_colour_zscore ($val)
                      : $is_prank  ? $map->get_colour_prank ($val)
+                     : $is_ratio  ? $map->get_colour_ratio ($val, $abs_extreme)
+                     : $is_divergent  ? $map->get_colour_divergent ($val, 0, $abs_extreme)
                      : $map->get_colour($val, $analysis_min, $analysis_max);
             }
             else {
@@ -956,6 +977,8 @@ sub recolour_cluster_elements {
     $map->get_legend->set_canape_mode($is_canape);
     $map->get_legend->set_zscore_mode($is_zscore);
     $map->get_legend->set_prank_mode($is_prank);
+    $map->get_legend->set_ratio_mode($is_ratio);
+    $map->get_legend->set_divergent_mode($is_divergent);
 
     if ($cluster_colour_mode eq 'list-values') {
         $map->set_legend_min_max($analysis_min, $analysis_max);
@@ -1235,12 +1258,32 @@ sub recolour_cluster_lines {
     my $analysis_min = $self->{analysis_min};
     my $analysis_max = $self->{analysis_max};
     my $colour_mode  = $self->get_cluster_colour_mode();
-
+
+    my %list_and_index = (list => $list_name, index => $list_index);
     my $is_canape = $list_name =~ />>CANAPE>>/ && $list_index =~ /^CANAPE/;
     my $is_zscore = eval {
-        $self->{parent_tab}->index_is_zscore (list => $list_name, index => $list_index);
+        $self->{parent_tab}->index_is_zscore (%list_and_index);
     };
     my $is_prank = $list_name =~ />>p_rank>>/;
+    my $is_ratio
+        = !$is_prank && !$is_zscore
+        && eval {$self->{parent_tab}->index_is_ratio(%list_and_index)};
+    my $is_divergent
+        = !$is_prank && !$is_zscore && !$is_ratio
+        && eval {$self->{parent_tab}->index_is_divergent(%list_and_index)};
+
+    my $abs_extreme;
+    if ($is_ratio) {
+        $abs_extreme = exp (max (abs log $analysis_min, log $analysis_max));
+        $analysis_min = 1 / $abs_extreme;
+        $analysis_max = $abs_extreme;
+    }
+    elsif ($is_divergent) {  #  assumes zero - needs work
+        $abs_extreme = max(abs $analysis_min, abs $analysis_max);
+        $analysis_min = 0;
+        $analysis_max = $abs_extreme;
+    }
+
 
     foreach my $node_ref (@$cluster_nodes) {
 
@@ -1264,10 +1307,12 @@ sub recolour_cluster_lines {
               : undef;  #  allows for missing lists
 
             $colour_ref = defined $val
-              ? (  $is_canape ? $map->get_colour_canape($val)
-                 : $is_zscore ? $map->get_colour_zscore($val)
-                 : $is_prank  ? $map->get_colour_prank($val)
-                 : $map->get_colour ($val, $analysis_min, $analysis_max)
+              ? (  $is_canape ? $map->get_colour_canape($val) :
+                   $is_zscore ? $map->get_colour_zscore($val) :
+                   $is_prank  ? $map->get_colour_prank($val) :
+                   $is_ratio  ? $map->get_colour_ratio ($val, $abs_extreme) :
+                   $is_divergent ? $map->get_colour_divergent ($val, 0, $abs_extreme) :
+                   $map->get_colour ($val, $analysis_min, $analysis_max)
                 )
               : undef;
         }
@@ -3111,6 +3156,7 @@ sub update_legend {
     return if !$legend;
 
     if ($self->{width_px} && $self->{height_px}) {
+        $legend->make_rect;
         $legend->reposition($self->{width_px}, $self->{height_px});
     }
 

diff --git a/lib/Biodiverse/GUI/Grid.pm b/lib/Biodiverse/GUI/Grid.pm
@@ -221,6 +221,7 @@ sub update_legend {
 
     return if !($self->{width_px} && $self->{height_px});
 
+    $self->get_legend->make_rect;
     $self->get_legend->reposition($self->{width_px}, $self->{height_px});
 
     return;
@@ -1134,6 +1135,7 @@ sub set_colour_for_undef {
     $self->{colour_none} = $colour;
 }
 
+#  need factory generation for the next few
 sub get_colour {
     my $self = shift;
     return $self->get_legend->get_colour (@_);
@@ -1154,6 +1156,15 @@ sub get_colour_prank {
     return $self->get_legend->get_colour_prank (@_);
 }
 
+sub get_colour_ratio {
+    my $self = shift;
+    return $self->get_legend->get_colour_ratio (@_);
+}
+
+sub get_colour_divergent {
+    my $self = shift;
+    return $self->get_legend->get_colour_divergent (@_);
+}
 
 
 ##########################################################