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Merge pull request #3 from WormBase/soba_multi
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check that roots have annotations or skip, but not for soba by ontolo…
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@raymond91125
raymond91125 authored Sep 24, 2019
2 parents ebeaf6a + 6d133e7 commit c9679f6
Showing 1 changed file with 11 additions and 10 deletions.
21 changes: 11 additions & 10 deletions soba_multi.cgi
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Original file line number Diff line number Diff line change
Expand Up @@ -1100,33 +1100,34 @@ sub annotSummaryJsonCode {
}


my $pieInfo = '';
my $geneOnePieSize = 0; my $geneTwoPieSize = 0;
my $geneOnePieOpacity = 0; my $geneTwoPieOpacity = 0;
if ($geneOneId) {
my $geneOnePieSize = $nodes{$node}{'counts'}{geneOne}{'anytype'} / $nodes{$node}{'counts'}{'anygene'}{'anytype'} * 100;
my $geneTwoPieSize = $nodes{$node}{'counts'}{geneTwo}{'anytype'} / $nodes{$node}{'counts'}{'anygene'}{'anytype'} * 100;
$geneOnePieSize = $nodes{$node}{'counts'}{geneOne}{'anytype'} / $nodes{$node}{'counts'}{'anygene'}{'anytype'} * 100;
$geneTwoPieSize = $nodes{$node}{'counts'}{geneTwo}{'anytype'} / $nodes{$node}{'counts'}{'anygene'}{'anytype'} * 100;
my $opacityMultiplier = 0.5;
my $geneOnePieOpacity = $nodes{$node}{'counts'}{geneOne}{'anytype'} / $anyRootNodeMaxAnnotationCount{geneOne} * $opacityMultiplier;
my $geneTwoPieOpacity = $nodes{$node}{'counts'}{geneTwo}{'anytype'} / $anyRootNodeMaxAnnotationCount{geneTwo} * $opacityMultiplier;
$pieInfo = qq("geneOnePieSize" : $geneOnePieSize, "geneTwoPieSize" : $geneTwoPieSize, "geneOnePieOpacity" : $geneOnePieOpacity, "geneTwoPieOpacity" : $geneTwoPieOpacity); }
$geneOnePieOpacity = $nodes{$node}{'counts'}{geneOne}{'anytype'} / $anyRootNodeMaxAnnotationCount{geneOne} * $opacityMultiplier;
$geneTwoPieOpacity = $nodes{$node}{'counts'}{geneTwo}{'anytype'} / $anyRootNodeMaxAnnotationCount{geneTwo} * $opacityMultiplier; }
my $pieInfo = qq(, "geneOnePieSize" : $geneOnePieSize, "geneTwoPieSize" : $geneTwoPieSize, "geneOnePieOpacity" : $geneOnePieOpacity, "geneTwoPieOpacity" : $geneTwoPieOpacity);

my $cytId = $node; $cytId =~ s/://;
if ($rootNodes{$node}) {
next unless ($nodes{$node}{'counts'}{'anygene'}{'anytype'}); # only add a root if it has annotations
next unless (($nodes{$node}{'counts'}{'anygene'}{'anytype'}) || ($objectsQvalue)); # only add a root if it has annotations or is soba by ontology terms, which don't have annoatations
my $nodeColor = 'blue'; if ($node eq 'GO:0000000') { $nodeColor = '#fff'; }
if ($goslimIds{$node}) { $backgroundColor = $nodeColor; }
# print qq(ROOT NODE $node\n);
# $node =~ s/GO://;
push @nodes, qq({ "data" : { "id" : "$cytId", "objId" : "$node", "name" : "$name", $annotCountsQvalue, "borderStyle" : "dashed", "labelColor" : "$labelColor", "nodeColor" : "$nodeColor", "annotationDirectness" : "inferred", "borderWidthUnweighted" : "$borderWidthRoot_unweighted", "borderWidthWeighted" : "$borderWidthRoot_weighted", "borderWidth" : "$borderWidthRoot", "fontSizeUnweighted" : "$fontSize_unweighted", "fontSizeWeighted" : "$fontSize_weighted", "fontSize" : "$fontSize", "diameter" : $diameter, "diameter_weighted" : $diameter_weighted, "diameter_unweighted" : $diameter_unweighted, "backgroundColor" : "$backgroundColor", "nodeShape" : "rectangle", "nodeExpandable" : "$nodeExpandable", $pieInfo } }); }
push @nodes, qq({ "data" : { "id" : "$cytId", "objId" : "$node", "name" : "$name", $annotCountsQvalue, "borderStyle" : "dashed", "labelColor" : "$labelColor", "nodeColor" : "$nodeColor", "annotationDirectness" : "inferred", "borderWidthUnweighted" : "$borderWidthRoot_unweighted", "borderWidthWeighted" : "$borderWidthRoot_weighted", "borderWidth" : "$borderWidthRoot", "fontSizeUnweighted" : "$fontSize_unweighted", "fontSizeWeighted" : "$fontSize_weighted", "fontSize" : "$fontSize", "diameter" : $diameter, "diameter_weighted" : $diameter_weighted, "diameter_unweighted" : $diameter_unweighted, "backgroundColor" : "$backgroundColor", "nodeShape" : "rectangle", "nodeExpandable" : "$nodeExpandable" $pieInfo } }); }
elsif ($nodes{$node}{lca}) {
# print qq(LCA NODE $node\n);
if ($goslimIds{$node}) { $backgroundColor = 'blue'; }
# $node =~ s/GO://;
push @nodes, qq({ "data" : { "id" : "$cytId", "objId" : "$node", "name" : "$name", $annotCountsQvalue, "borderStyle" : "dashed", "labelColor" : "$labelColor", "nodeColor" : "blue", "annotationDirectness" : "inferred", "borderWidthUnweighted" : "$borderWidth_unweighted", "borderWidthWeighted" : "$borderWidth_weighted", "borderWidth" : "$borderWidth", "fontSizeUnweighted" : "$fontSize_unweighted", "fontSizeWeighted" : "$fontSize_weighted", "fontSize" : "$fontSize", "diameter" : $diameter, "diameter_weighted" : $diameter_weighted, "diameter_unweighted" : $diameter_unweighted, "backgroundColor" : "$backgroundColor", "nodeShape" : "ellipse", "nodeExpandable" : "$nodeExpandable", $pieInfo } }); }
push @nodes, qq({ "data" : { "id" : "$cytId", "objId" : "$node", "name" : "$name", $annotCountsQvalue, "borderStyle" : "dashed", "labelColor" : "$labelColor", "nodeColor" : "blue", "annotationDirectness" : "inferred", "borderWidthUnweighted" : "$borderWidth_unweighted", "borderWidthWeighted" : "$borderWidth_weighted", "borderWidth" : "$borderWidth", "fontSizeUnweighted" : "$fontSize_unweighted", "fontSizeWeighted" : "$fontSize_weighted", "fontSize" : "$fontSize", "diameter" : $diameter, "diameter_weighted" : $diameter_weighted, "diameter_unweighted" : $diameter_unweighted, "backgroundColor" : "$backgroundColor", "nodeShape" : "ellipse", "nodeExpandable" : "$nodeExpandable" $pieInfo } }); }
elsif ($nodes{$node}{annot}) {
# print qq(ANNOT NODE $node\n);
if ($goslimIds{$node}) { $backgroundColor = 'red'; }
# $node =~ s/GO://;
push @nodes, qq({ "data" : { "id" : "$cytId", "objId" : "$node", "name" : "$name", $annotCountsQvalue, "borderStyle" : "solid", "labelColor" : "$labelColor", "nodeColor" : "red", "annotationDirectness" : "direct", "borderWidthUnweighted" : "$borderWidth_unweighted", "borderWidthWeighted" : "$borderWidth_weighted", "borderWidth" : "$borderWidth", "fontSizeUnweighted" : "$fontSize_unweighted", "fontSizeWeighted" : "$fontSize_weighted", "fontSize" : "$fontSize", "diameter" : $diameter, "diameter_weighted" : $diameter_weighted, "diameter_unweighted" : $diameter_unweighted, "backgroundColor" : "$backgroundColor", "nodeShape" : "ellipse", "nodeExpandable" : "$nodeExpandable", $pieInfo } }); }
push @nodes, qq({ "data" : { "id" : "$cytId", "objId" : "$node", "name" : "$name", $annotCountsQvalue, "borderStyle" : "solid", "labelColor" : "$labelColor", "nodeColor" : "red", "annotationDirectness" : "direct", "borderWidthUnweighted" : "$borderWidth_unweighted", "borderWidthWeighted" : "$borderWidth_weighted", "borderWidth" : "$borderWidth", "fontSizeUnweighted" : "$fontSize_unweighted", "fontSizeWeighted" : "$fontSize_weighted", "fontSize" : "$fontSize", "diameter" : $diameter, "diameter_weighted" : $diameter_weighted, "diameter_unweighted" : $diameter_unweighted, "backgroundColor" : "$backgroundColor", "nodeShape" : "ellipse", "nodeExpandable" : "$nodeExpandable" $pieInfo } }); }
else {
# print qq(OTHER NODE $node\n);
}
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