Similarity Heatmap

Notice (8): Undefined variable: source_groups_information [APP/View/Tools/similarity_heatmap.ctp, line 77]
Code Context
                    <label>Source(s)</label>

                    <select class='form form-select' name='ontology_source_group' id='ontology_source_group'>

                        <?php foreach ($source_groups_information['available'] as $source_group_id) : ?>
$viewFile = '/www/bioinformatics01_ro/plaza/instances/monocots_05/app/View/Tools/similarity_heatmap.ctp'
$dataForView = array(
	'navigation_bar_info' => array(
		'num_colinearity_runs' => (int) 3,
		'num_colinearity_with_dating_runs' => (int) 2,
		'num_functional_clusters_runs' => (int) 6,
		'has_pan_genomes' => false
	),
	'gene_selection' => array(
		'parameters' => array(),
		'genes' => array()
	),
	'all_species' => array(
		'ata' => array(
			'species' => 'ata',
			'common_name' => 'Aegilops tauschii',
			'tax_id' => '37682',
			'version' => 'Aet V4.0'
		),
		'asa' => array(
			'species' => 'asa',
			'common_name' => 'Allium sativum',
			'tax_id' => '4682',
			'version' => 'V1.0'
		),
		'atr' => array(
			'species' => 'atr',
			'common_name' => 'Amborella trichopoda',
			'tax_id' => '13333',
			'version' => 'JGI v1.0'
		),
		'aco' => array(
			'species' => 'aco',
			'common_name' => 'Ananas comosus',
			'tax_id' => '4615',
			'version' => 'JGI v3.0'
		),
		'aag' => array(
			'species' => 'aag',
			'common_name' => 'Anthoceros agrestis',
			'tax_id' => '41834',
			'version' => 'v1.1'
		),
		'ath' => array(
			'species' => 'ath',
			'common_name' => 'Arabidopsis thaliana',
			'tax_id' => '3702',
			'version' => 'Araport11'
		),
		'aof' => array(
			'species' => 'aof',
			'common_name' => 'Asparagus officinalis',
			'tax_id' => '4686',
			'version' => 'v1.1'
		),
		'bdi' => array(
			'species' => 'bdi',
			'common_name' => 'Brachypodium distachyon',
			'tax_id' => '15368',
			'version' => 'JGI v3.2'
		),
		'calsi' => array(
			'species' => 'calsi',
			'common_name' => 'Calamus simplicifolius',
			'tax_id' => '746888',
			'version' => 'v1.0'
		),
		'cpu' => array(
			'species' => 'cpu',
			'common_name' => 'Cenchrus purpureus',
			'tax_id' => '154765',
			'version' => 'v1.0'
		),
		'cde' => array(
			'species' => 'cde',
			'common_name' => 'Ceratophyllum demersum',
			'tax_id' => '4428',
			'version' => 'v1.0'
		),
		'cbr' => array(
			'species' => 'cbr',
			'common_name' => 'Chara braunii',
			'tax_id' => '69332',
			'version' => 'Cbr1.0'
		),
		'cre' => array(
			'species' => 'cre',
			'common_name' => 'Chlamydomonas reinhardtii',
			'tax_id' => '3055',
			'version' => 'JGI v5.5'
		),
		'dex' => array(
			'species' => 'dex',
			'common_name' => 'Digitaria exilis',
			'tax_id' => '1010633',
			'version' => 'Dexi_CM05836 v1'
		),
		'ddu' => array(
			'species' => 'ddu',
			'common_name' => 'Dioscorea dumetorum',
			'tax_id' => '167584',
			'version' => 'Trifoliate Yam v1.0'
		),
		'egu' => array(
			'species' => 'egu',
			'common_name' => 'Elaeis guineensis',
			'tax_id' => '51953',
			'version' => 'EG5.1'
		),
		'ecu' => array(
			'species' => 'ecu',
			'common_name' => 'Eragrostis curvula',
			'tax_id' => '38414',
			'version' => 'CERZOS_E.curvula1.0'
		),
		'gma' => array(
			'species' => 'gma',
			'common_name' => 'Glycine max',
			'tax_id' => '3847',
			'version' => 'JGI Wm82.a4.v1'
		),
		'hvu' => array(
			'species' => 'hvu',
			'common_name' => 'Hordeum vulgare',
			'tax_id' => '4513',
			'version' => 'Morex v2'
		),
		'lpe' => array(
			'species' => 'lpe',
			'common_name' => 'Lolium perenne',
			'tax_id' => '4522',
			'version' => '2.6.1-v3'
		),
		'mbi' => array(
			'species' => 'mbi',
			'common_name' => 'Magnolia biondii',
			'tax_id' => '86725',
			'version' => 'v1.0'
		),
		'mpo' => array(
			'species' => 'mpo',
			'common_name' => 'Marchantia polymorpha',
			'tax_id' => '3197',
			'version' => 'JGI v3.1'
		),
		'mco' => array(
			'species' => 'mco',
			'common_name' => 'Micromonas commoda',
			'tax_id' => '296587',
			'version' => 'JGI v3.0'
		),
		'msi' => array(
			'species' => 'msi',
			'common_name' => 'Miscanthus sinensis',
			'tax_id' => '62337',
			'version' => 'v7.1'
		),
		'mac' => array(
			'species' => 'mac',
			'common_name' => 'Musa acuminata',
			'tax_id' => '4641',
			'version' => 'Banana Genome v2.0'
		),
		'oth' => array(
			'species' => 'oth',
			'common_name' => 'Oropetium thomaeum',
			'tax_id' => '1148796',
			'version' => 'COGE v2.0'
		),
		'oal' => array(
			'species' => 'oal',
			'common_name' => 'Oryza alta',
			'tax_id' => '52545',
			'version' => 'OAv1'
		),
		'obr' => array(
			'species' => 'obr',
			'common_name' => 'Oryza brachyantha',
			'tax_id' => '4533',
			'version' => 'Ensembl Plants v1.4b'
		),
		'osak' => array(
			'species' => 'osak',
			'common_name' => 'Oryza sativa Kitaake',
			'tax_id' => '4530',
			'version' => 'V3.2'
		),
		'osaindica' => array(
			'species' => 'osaindica',
			'common_name' => 'Oryza sativa ssp. indica',
			'tax_id' => '39946',
			'version' => 'MBKBASE v1.0'
		),
		'osa' => array(
			'species' => 'osa',
			'common_name' => 'Oryza sativa ssp. japonica',
			'tax_id' => '39947',
			'version' => 'IRGSP-1.0-2021-05-10'
		),
		'pha' => array(
			'species' => 'pha',
			'common_name' => 'Panicum hallii',
			'tax_id' => '206008',
			'version' => 'JGI v3.2'
		),
		'ped' => array(
			'species' => 'ped',
			'common_name' => 'Phyllostachys edulis',
			'tax_id' => '38705',
			'version' => 'GigaDBv2.0'
		),
		'ppa' => array(
			'species' => 'ppa',
			'common_name' => 'Physcomitrium patens',
			'tax_id' => '3218',
			'version' => 'JGI v3.3'
		),
		'ptr' => array(
			'species' => 'ptr',
			'common_name' => 'Populus trichocarpa',
			'tax_id' => '3694',
			'version' => 'JGI v4.1'
		),
		'pco' => array(
			'species' => 'pco',
			'common_name' => 'Prasinoderma coloniale',
			'tax_id' => '156133',
			'version' => 'v1.0'
		),
		'ssp' => array(
			'species' => 'ssp',
			'common_name' => 'Saccharum spontaneum',
			'tax_id' => '62335',
			'version' => 'v20190103'
		),
		'sce' => array(
			'species' => 'sce',
			'common_name' => 'Secale cereale',
			'tax_id' => '4550',
			'version' => 'Rye v1.0'
		),
		'smo' => array(
			'species' => 'smo',
			'common_name' => 'Selaginella moellendorffii',
			'tax_id' => '88036',
			'version' => 'v1.0'
		),
		'sgi' => array(
			'species' => 'sgi',
			'common_name' => 'Sequoiadendron giganteum',
			'tax_id' => '99814',
			'version' => 'V2.0'
		),
		'sit' => array(
			'species' => 'sit',
			'common_name' => 'Setaria italica',
			'tax_id' => '4555',
			'version' => 'JGI v2.2'
		),
		'svi' => array(
			'species' => 'svi',
			'common_name' => 'Setaria viridis',
			'tax_id' => '4556',
			'version' => 'Phytozome v2.1'
		),
		'sly' => array(
			'species' => 'sly',
			'common_name' => 'Solanum lycopersicum',
			'tax_id' => '4081',
			'version' => 'ITAG4.0'
		),
		'sbi' => array(
			'species' => 'sbi',
			'common_name' => 'Sorghum bicolor',
			'tax_id' => '4558',
			'version' => 'JGI v3.1'
		),
		'spo' => array(
			'species' => 'spo',
			'common_name' => 'Spirodela polyrhiza',
			'tax_id' => '29656',
			'version' => 'JGI v2.0'
		),
		'tae' => array(
			'species' => 'tae',
			'common_name' => 'Triticum aestivum',
			'tax_id' => '4565',
			'version' => 'IWGSCv2.1'
		),
		'tdi' => array(
			'species' => 'tdi',
			'common_name' => 'Triticum dicoccoides',
			'tax_id' => '85692',
			'version' => 'Ensembl'
		),
		'ttu' => array(
			'species' => 'ttu',
			'common_name' => 'Triticum turgidum',
			'tax_id' => '4567',
			'version' => 'v1.0'
		),
		'vpl' => array(
			'species' => 'vpl',
			'common_name' => 'Vanilla planifolia',
			'tax_id' => '51239',
			'version' => 'Elo Vpla-A Principal v1.0'
		),
		'zma' => array(
			'species' => 'zma',
			'common_name' => 'Zea mays B73',
			'tax_id' => '4577',
			'version' => 'NAM v5.0'
		),
		'zma-b104' => array(
			'species' => 'zma-b104',
			'common_name' => 'Zea mays B104',
			'tax_id' => '4577',
			'version' => 'v1.0'
		),
		'zosmarina' => array(
			'species' => 'zosmarina',
			'common_name' => 'Zostera marina',
			'tax_id' => '29655',
			'version' => 'v3.1'
		),
		'zjn' => array(
			'species' => 'zjn',
			'common_name' => 'Zoysia japonica ssp. nagirizaki',
			'tax_id' => '309978',
			'version' => 'Zoysia Genome Database v1.1'
		)
	),
	'subfamily_family_types' => array(
		(int) 0 => 'ORTHOFAM'
	),
	'parental_family_types' => array(
		(int) 0 => 'HOMFAM'
	),
	'gene_family_types_information' => array(
		'HOMFAM' => array(
			'id' => 'HOMFAM',
			'name' => 'Homologous gene family',
			'gene_type' => 'coding',
			'parent_id' => '',
			'ancestry' => 'homology'
		),
		'ORTHOFAM' => array(
			'id' => 'ORTHOFAM',
			'name' => 'Orthologous gene family',
			'gene_type' => 'coding',
			'parent_id' => 'HOMFAM',
			'ancestry' => 'orthology'
		)
	),
	'allowed_data_types' => array(
		'GO' => 'Gene Ontology',
		'INTERPRO' => 'InterPro',
		'GENE_FAMILY' => 'Gene Family'
	)
)
$navigation_bar_info = array(
	'num_colinearity_runs' => (int) 3,
	'num_colinearity_with_dating_runs' => (int) 2,
	'num_functional_clusters_runs' => (int) 6,
	'has_pan_genomes' => false
)
$gene_selection = array(
	'parameters' => array(),
	'genes' => array()
)
$all_species = array(
	'ata' => array(
		'species' => 'ata',
		'common_name' => 'Aegilops tauschii',
		'tax_id' => '37682',
		'version' => 'Aet V4.0'
	),
	'asa' => array(
		'species' => 'asa',
		'common_name' => 'Allium sativum',
		'tax_id' => '4682',
		'version' => 'V1.0'
	),
	'atr' => array(
		'species' => 'atr',
		'common_name' => 'Amborella trichopoda',
		'tax_id' => '13333',
		'version' => 'JGI v1.0'
	),
	'aco' => array(
		'species' => 'aco',
		'common_name' => 'Ananas comosus',
		'tax_id' => '4615',
		'version' => 'JGI v3.0'
	),
	'aag' => array(
		'species' => 'aag',
		'common_name' => 'Anthoceros agrestis',
		'tax_id' => '41834',
		'version' => 'v1.1'
	),
	'ath' => array(
		'species' => 'ath',
		'common_name' => 'Arabidopsis thaliana',
		'tax_id' => '3702',
		'version' => 'Araport11'
	),
	'aof' => array(
		'species' => 'aof',
		'common_name' => 'Asparagus officinalis',
		'tax_id' => '4686',
		'version' => 'v1.1'
	),
	'bdi' => array(
		'species' => 'bdi',
		'common_name' => 'Brachypodium distachyon',
		'tax_id' => '15368',
		'version' => 'JGI v3.2'
	),
	'calsi' => array(
		'species' => 'calsi',
		'common_name' => 'Calamus simplicifolius',
		'tax_id' => '746888',
		'version' => 'v1.0'
	),
	'cpu' => array(
		'species' => 'cpu',
		'common_name' => 'Cenchrus purpureus',
		'tax_id' => '154765',
		'version' => 'v1.0'
	),
	'cde' => array(
		'species' => 'cde',
		'common_name' => 'Ceratophyllum demersum',
		'tax_id' => '4428',
		'version' => 'v1.0'
	),
	'cbr' => array(
		'species' => 'cbr',
		'common_name' => 'Chara braunii',
		'tax_id' => '69332',
		'version' => 'Cbr1.0'
	),
	'cre' => array(
		'species' => 'cre',
		'common_name' => 'Chlamydomonas reinhardtii',
		'tax_id' => '3055',
		'version' => 'JGI v5.5'
	),
	'dex' => array(
		'species' => 'dex',
		'common_name' => 'Digitaria exilis',
		'tax_id' => '1010633',
		'version' => 'Dexi_CM05836 v1'
	),
	'ddu' => array(
		'species' => 'ddu',
		'common_name' => 'Dioscorea dumetorum',
		'tax_id' => '167584',
		'version' => 'Trifoliate Yam v1.0'
	),
	'egu' => array(
		'species' => 'egu',
		'common_name' => 'Elaeis guineensis',
		'tax_id' => '51953',
		'version' => 'EG5.1'
	),
	'ecu' => array(
		'species' => 'ecu',
		'common_name' => 'Eragrostis curvula',
		'tax_id' => '38414',
		'version' => 'CERZOS_E.curvula1.0'
	),
	'gma' => array(
		'species' => 'gma',
		'common_name' => 'Glycine max',
		'tax_id' => '3847',
		'version' => 'JGI Wm82.a4.v1'
	),
	'hvu' => array(
		'species' => 'hvu',
		'common_name' => 'Hordeum vulgare',
		'tax_id' => '4513',
		'version' => 'Morex v2'
	),
	'lpe' => array(
		'species' => 'lpe',
		'common_name' => 'Lolium perenne',
		'tax_id' => '4522',
		'version' => '2.6.1-v3'
	),
	'mbi' => array(
		'species' => 'mbi',
		'common_name' => 'Magnolia biondii',
		'tax_id' => '86725',
		'version' => 'v1.0'
	),
	'mpo' => array(
		'species' => 'mpo',
		'common_name' => 'Marchantia polymorpha',
		'tax_id' => '3197',
		'version' => 'JGI v3.1'
	),
	'mco' => array(
		'species' => 'mco',
		'common_name' => 'Micromonas commoda',
		'tax_id' => '296587',
		'version' => 'JGI v3.0'
	),
	'msi' => array(
		'species' => 'msi',
		'common_name' => 'Miscanthus sinensis',
		'tax_id' => '62337',
		'version' => 'v7.1'
	),
	'mac' => array(
		'species' => 'mac',
		'common_name' => 'Musa acuminata',
		'tax_id' => '4641',
		'version' => 'Banana Genome v2.0'
	),
	'oth' => array(
		'species' => 'oth',
		'common_name' => 'Oropetium thomaeum',
		'tax_id' => '1148796',
		'version' => 'COGE v2.0'
	),
	'oal' => array(
		'species' => 'oal',
		'common_name' => 'Oryza alta',
		'tax_id' => '52545',
		'version' => 'OAv1'
	),
	'obr' => array(
		'species' => 'obr',
		'common_name' => 'Oryza brachyantha',
		'tax_id' => '4533',
		'version' => 'Ensembl Plants v1.4b'
	),
	'osak' => array(
		'species' => 'osak',
		'common_name' => 'Oryza sativa Kitaake',
		'tax_id' => '4530',
		'version' => 'V3.2'
	),
	'osaindica' => array(
		'species' => 'osaindica',
		'common_name' => 'Oryza sativa ssp. indica',
		'tax_id' => '39946',
		'version' => 'MBKBASE v1.0'
	),
	'osa' => array(
		'species' => 'osa',
		'common_name' => 'Oryza sativa ssp. japonica',
		'tax_id' => '39947',
		'version' => 'IRGSP-1.0-2021-05-10'
	),
	'pha' => array(
		'species' => 'pha',
		'common_name' => 'Panicum hallii',
		'tax_id' => '206008',
		'version' => 'JGI v3.2'
	),
	'ped' => array(
		'species' => 'ped',
		'common_name' => 'Phyllostachys edulis',
		'tax_id' => '38705',
		'version' => 'GigaDBv2.0'
	),
	'ppa' => array(
		'species' => 'ppa',
		'common_name' => 'Physcomitrium patens',
		'tax_id' => '3218',
		'version' => 'JGI v3.3'
	),
	'ptr' => array(
		'species' => 'ptr',
		'common_name' => 'Populus trichocarpa',
		'tax_id' => '3694',
		'version' => 'JGI v4.1'
	),
	'pco' => array(
		'species' => 'pco',
		'common_name' => 'Prasinoderma coloniale',
		'tax_id' => '156133',
		'version' => 'v1.0'
	),
	'ssp' => array(
		'species' => 'ssp',
		'common_name' => 'Saccharum spontaneum',
		'tax_id' => '62335',
		'version' => 'v20190103'
	),
	'sce' => array(
		'species' => 'sce',
		'common_name' => 'Secale cereale',
		'tax_id' => '4550',
		'version' => 'Rye v1.0'
	),
	'smo' => array(
		'species' => 'smo',
		'common_name' => 'Selaginella moellendorffii',
		'tax_id' => '88036',
		'version' => 'v1.0'
	),
	'sgi' => array(
		'species' => 'sgi',
		'common_name' => 'Sequoiadendron giganteum',
		'tax_id' => '99814',
		'version' => 'V2.0'
	),
	'sit' => array(
		'species' => 'sit',
		'common_name' => 'Setaria italica',
		'tax_id' => '4555',
		'version' => 'JGI v2.2'
	),
	'svi' => array(
		'species' => 'svi',
		'common_name' => 'Setaria viridis',
		'tax_id' => '4556',
		'version' => 'Phytozome v2.1'
	),
	'sly' => array(
		'species' => 'sly',
		'common_name' => 'Solanum lycopersicum',
		'tax_id' => '4081',
		'version' => 'ITAG4.0'
	),
	'sbi' => array(
		'species' => 'sbi',
		'common_name' => 'Sorghum bicolor',
		'tax_id' => '4558',
		'version' => 'JGI v3.1'
	),
	'spo' => array(
		'species' => 'spo',
		'common_name' => 'Spirodela polyrhiza',
		'tax_id' => '29656',
		'version' => 'JGI v2.0'
	),
	'tae' => array(
		'species' => 'tae',
		'common_name' => 'Triticum aestivum',
		'tax_id' => '4565',
		'version' => 'IWGSCv2.1'
	),
	'tdi' => array(
		'species' => 'tdi',
		'common_name' => 'Triticum dicoccoides',
		'tax_id' => '85692',
		'version' => 'Ensembl'
	),
	'ttu' => array(
		'species' => 'ttu',
		'common_name' => 'Triticum turgidum',
		'tax_id' => '4567',
		'version' => 'v1.0'
	),
	'vpl' => array(
		'species' => 'vpl',
		'common_name' => 'Vanilla planifolia',
		'tax_id' => '51239',
		'version' => 'Elo Vpla-A Principal v1.0'
	),
	'zma' => array(
		'species' => 'zma',
		'common_name' => 'Zea mays B73',
		'tax_id' => '4577',
		'version' => 'NAM v5.0'
	),
	'zma-b104' => array(
		'species' => 'zma-b104',
		'common_name' => 'Zea mays B104',
		'tax_id' => '4577',
		'version' => 'v1.0'
	),
	'zosmarina' => array(
		'species' => 'zosmarina',
		'common_name' => 'Zostera marina',
		'tax_id' => '29655',
		'version' => 'v3.1'
	),
	'zjn' => array(
		'species' => 'zjn',
		'common_name' => 'Zoysia japonica ssp. nagirizaki',
		'tax_id' => '309978',
		'version' => 'Zoysia Genome Database v1.1'
	)
)
$subfamily_family_types = array(
	(int) 0 => 'ORTHOFAM'
)
$parental_family_types = array(
	(int) 0 => 'HOMFAM'
)
$gene_family_types_information = array(
	'HOMFAM' => array(
		'id' => 'HOMFAM',
		'name' => 'Homologous gene family',
		'gene_type' => 'coding',
		'parent_id' => '',
		'ancestry' => 'homology'
	),
	'ORTHOFAM' => array(
		'id' => 'ORTHOFAM',
		'name' => 'Orthologous gene family',
		'gene_type' => 'coding',
		'parent_id' => 'HOMFAM',
		'ancestry' => 'orthology'
	)
)
$allowed_data_types = array(
	'GO' => 'Gene Ontology',
	'INTERPRO' => 'InterPro',
	'GENE_FAMILY' => 'Gene Family'
)
$data_identifier_value = ''
$data_identifier_description = ''
$adt_title = 'Gene Family'
$adt = 'GENE_FAMILY'
$is_selected = null
include - APP/View/Tools/similarity_heatmap.ctp, line 77
View::_evaluate() - CORE/Cake/View/View.php, line 971
View::_render() - CORE/Cake/View/View.php, line 933
View::render() - CORE/Cake/View/View.php, line 473
Controller::render() - CORE/Cake/Controller/Controller.php, line 963
Dispatcher::_invoke() - CORE/Cake/Routing/Dispatcher.php, line 200
Dispatcher::dispatch() - CORE/Cake/Routing/Dispatcher.php, line 167
[main] - APP/webroot/index.php, line 149

Notice (8): Trying to access array offset on value of type null [APP/View/Tools/similarity_heatmap.ctp, line 77]
Code Context
                    <label>Source(s)</label>

                    <select class='form form-select' name='ontology_source_group' id='ontology_source_group'>

                        <?php foreach ($source_groups_information['available'] as $source_group_id) : ?>
$viewFile = '/www/bioinformatics01_ro/plaza/instances/monocots_05/app/View/Tools/similarity_heatmap.ctp'
$dataForView = array(
	'navigation_bar_info' => array(
		'num_colinearity_runs' => (int) 3,
		'num_colinearity_with_dating_runs' => (int) 2,
		'num_functional_clusters_runs' => (int) 6,
		'has_pan_genomes' => false
	),
	'gene_selection' => array(
		'parameters' => array(),
		'genes' => array()
	),
	'all_species' => array(
		'ata' => array(
			'species' => 'ata',
			'common_name' => 'Aegilops tauschii',
			'tax_id' => '37682',
			'version' => 'Aet V4.0'
		),
		'asa' => array(
			'species' => 'asa',
			'common_name' => 'Allium sativum',
			'tax_id' => '4682',
			'version' => 'V1.0'
		),
		'atr' => array(
			'species' => 'atr',
			'common_name' => 'Amborella trichopoda',
			'tax_id' => '13333',
			'version' => 'JGI v1.0'
		),
		'aco' => array(
			'species' => 'aco',
			'common_name' => 'Ananas comosus',
			'tax_id' => '4615',
			'version' => 'JGI v3.0'
		),
		'aag' => array(
			'species' => 'aag',
			'common_name' => 'Anthoceros agrestis',
			'tax_id' => '41834',
			'version' => 'v1.1'
		),
		'ath' => array(
			'species' => 'ath',
			'common_name' => 'Arabidopsis thaliana',
			'tax_id' => '3702',
			'version' => 'Araport11'
		),
		'aof' => array(
			'species' => 'aof',
			'common_name' => 'Asparagus officinalis',
			'tax_id' => '4686',
			'version' => 'v1.1'
		),
		'bdi' => array(
			'species' => 'bdi',
			'common_name' => 'Brachypodium distachyon',
			'tax_id' => '15368',
			'version' => 'JGI v3.2'
		),
		'calsi' => array(
			'species' => 'calsi',
			'common_name' => 'Calamus simplicifolius',
			'tax_id' => '746888',
			'version' => 'v1.0'
		),
		'cpu' => array(
			'species' => 'cpu',
			'common_name' => 'Cenchrus purpureus',
			'tax_id' => '154765',
			'version' => 'v1.0'
		),
		'cde' => array(
			'species' => 'cde',
			'common_name' => 'Ceratophyllum demersum',
			'tax_id' => '4428',
			'version' => 'v1.0'
		),
		'cbr' => array(
			'species' => 'cbr',
			'common_name' => 'Chara braunii',
			'tax_id' => '69332',
			'version' => 'Cbr1.0'
		),
		'cre' => array(
			'species' => 'cre',
			'common_name' => 'Chlamydomonas reinhardtii',
			'tax_id' => '3055',
			'version' => 'JGI v5.5'
		),
		'dex' => array(
			'species' => 'dex',
			'common_name' => 'Digitaria exilis',
			'tax_id' => '1010633',
			'version' => 'Dexi_CM05836 v1'
		),
		'ddu' => array(
			'species' => 'ddu',
			'common_name' => 'Dioscorea dumetorum',
			'tax_id' => '167584',
			'version' => 'Trifoliate Yam v1.0'
		),
		'egu' => array(
			'species' => 'egu',
			'common_name' => 'Elaeis guineensis',
			'tax_id' => '51953',
			'version' => 'EG5.1'
		),
		'ecu' => array(
			'species' => 'ecu',
			'common_name' => 'Eragrostis curvula',
			'tax_id' => '38414',
			'version' => 'CERZOS_E.curvula1.0'
		),
		'gma' => array(
			'species' => 'gma',
			'common_name' => 'Glycine max',
			'tax_id' => '3847',
			'version' => 'JGI Wm82.a4.v1'
		),
		'hvu' => array(
			'species' => 'hvu',
			'common_name' => 'Hordeum vulgare',
			'tax_id' => '4513',
			'version' => 'Morex v2'
		),
		'lpe' => array(
			'species' => 'lpe',
			'common_name' => 'Lolium perenne',
			'tax_id' => '4522',
			'version' => '2.6.1-v3'
		),
		'mbi' => array(
			'species' => 'mbi',
			'common_name' => 'Magnolia biondii',
			'tax_id' => '86725',
			'version' => 'v1.0'
		),
		'mpo' => array(
			'species' => 'mpo',
			'common_name' => 'Marchantia polymorpha',
			'tax_id' => '3197',
			'version' => 'JGI v3.1'
		),
		'mco' => array(
			'species' => 'mco',
			'common_name' => 'Micromonas commoda',
			'tax_id' => '296587',
			'version' => 'JGI v3.0'
		),
		'msi' => array(
			'species' => 'msi',
			'common_name' => 'Miscanthus sinensis',
			'tax_id' => '62337',
			'version' => 'v7.1'
		),
		'mac' => array(
			'species' => 'mac',
			'common_name' => 'Musa acuminata',
			'tax_id' => '4641',
			'version' => 'Banana Genome v2.0'
		),
		'oth' => array(
			'species' => 'oth',
			'common_name' => 'Oropetium thomaeum',
			'tax_id' => '1148796',
			'version' => 'COGE v2.0'
		),
		'oal' => array(
			'species' => 'oal',
			'common_name' => 'Oryza alta',
			'tax_id' => '52545',
			'version' => 'OAv1'
		),
		'obr' => array(
			'species' => 'obr',
			'common_name' => 'Oryza brachyantha',
			'tax_id' => '4533',
			'version' => 'Ensembl Plants v1.4b'
		),
		'osak' => array(
			'species' => 'osak',
			'common_name' => 'Oryza sativa Kitaake',
			'tax_id' => '4530',
			'version' => 'V3.2'
		),
		'osaindica' => array(
			'species' => 'osaindica',
			'common_name' => 'Oryza sativa ssp. indica',
			'tax_id' => '39946',
			'version' => 'MBKBASE v1.0'
		),
		'osa' => array(
			'species' => 'osa',
			'common_name' => 'Oryza sativa ssp. japonica',
			'tax_id' => '39947',
			'version' => 'IRGSP-1.0-2021-05-10'
		),
		'pha' => array(
			'species' => 'pha',
			'common_name' => 'Panicum hallii',
			'tax_id' => '206008',
			'version' => 'JGI v3.2'
		),
		'ped' => array(
			'species' => 'ped',
			'common_name' => 'Phyllostachys edulis',
			'tax_id' => '38705',
			'version' => 'GigaDBv2.0'
		),
		'ppa' => array(
			'species' => 'ppa',
			'common_name' => 'Physcomitrium patens',
			'tax_id' => '3218',
			'version' => 'JGI v3.3'
		),
		'ptr' => array(
			'species' => 'ptr',
			'common_name' => 'Populus trichocarpa',
			'tax_id' => '3694',
			'version' => 'JGI v4.1'
		),
		'pco' => array(
			'species' => 'pco',
			'common_name' => 'Prasinoderma coloniale',
			'tax_id' => '156133',
			'version' => 'v1.0'
		),
		'ssp' => array(
			'species' => 'ssp',
			'common_name' => 'Saccharum spontaneum',
			'tax_id' => '62335',
			'version' => 'v20190103'
		),
		'sce' => array(
			'species' => 'sce',
			'common_name' => 'Secale cereale',
			'tax_id' => '4550',
			'version' => 'Rye v1.0'
		),
		'smo' => array(
			'species' => 'smo',
			'common_name' => 'Selaginella moellendorffii',
			'tax_id' => '88036',
			'version' => 'v1.0'
		),
		'sgi' => array(
			'species' => 'sgi',
			'common_name' => 'Sequoiadendron giganteum',
			'tax_id' => '99814',
			'version' => 'V2.0'
		),
		'sit' => array(
			'species' => 'sit',
			'common_name' => 'Setaria italica',
			'tax_id' => '4555',
			'version' => 'JGI v2.2'
		),
		'svi' => array(
			'species' => 'svi',
			'common_name' => 'Setaria viridis',
			'tax_id' => '4556',
			'version' => 'Phytozome v2.1'
		),
		'sly' => array(
			'species' => 'sly',
			'common_name' => 'Solanum lycopersicum',
			'tax_id' => '4081',
			'version' => 'ITAG4.0'
		),
		'sbi' => array(
			'species' => 'sbi',
			'common_name' => 'Sorghum bicolor',
			'tax_id' => '4558',
			'version' => 'JGI v3.1'
		),
		'spo' => array(
			'species' => 'spo',
			'common_name' => 'Spirodela polyrhiza',
			'tax_id' => '29656',
			'version' => 'JGI v2.0'
		),
		'tae' => array(
			'species' => 'tae',
			'common_name' => 'Triticum aestivum',
			'tax_id' => '4565',
			'version' => 'IWGSCv2.1'
		),
		'tdi' => array(
			'species' => 'tdi',
			'common_name' => 'Triticum dicoccoides',
			'tax_id' => '85692',
			'version' => 'Ensembl'
		),
		'ttu' => array(
			'species' => 'ttu',
			'common_name' => 'Triticum turgidum',
			'tax_id' => '4567',
			'version' => 'v1.0'
		),
		'vpl' => array(
			'species' => 'vpl',
			'common_name' => 'Vanilla planifolia',
			'tax_id' => '51239',
			'version' => 'Elo Vpla-A Principal v1.0'
		),
		'zma' => array(
			'species' => 'zma',
			'common_name' => 'Zea mays B73',
			'tax_id' => '4577',
			'version' => 'NAM v5.0'
		),
		'zma-b104' => array(
			'species' => 'zma-b104',
			'common_name' => 'Zea mays B104',
			'tax_id' => '4577',
			'version' => 'v1.0'
		),
		'zosmarina' => array(
			'species' => 'zosmarina',
			'common_name' => 'Zostera marina',
			'tax_id' => '29655',
			'version' => 'v3.1'
		),
		'zjn' => array(
			'species' => 'zjn',
			'common_name' => 'Zoysia japonica ssp. nagirizaki',
			'tax_id' => '309978',
			'version' => 'Zoysia Genome Database v1.1'
		)
	),
	'subfamily_family_types' => array(
		(int) 0 => 'ORTHOFAM'
	),
	'parental_family_types' => array(
		(int) 0 => 'HOMFAM'
	),
	'gene_family_types_information' => array(
		'HOMFAM' => array(
			'id' => 'HOMFAM',
			'name' => 'Homologous gene family',
			'gene_type' => 'coding',
			'parent_id' => '',
			'ancestry' => 'homology'
		),
		'ORTHOFAM' => array(
			'id' => 'ORTHOFAM',
			'name' => 'Orthologous gene family',
			'gene_type' => 'coding',
			'parent_id' => 'HOMFAM',
			'ancestry' => 'orthology'
		)
	),
	'allowed_data_types' => array(
		'GO' => 'Gene Ontology',
		'INTERPRO' => 'InterPro',
		'GENE_FAMILY' => 'Gene Family'
	)
)
$navigation_bar_info = array(
	'num_colinearity_runs' => (int) 3,
	'num_colinearity_with_dating_runs' => (int) 2,
	'num_functional_clusters_runs' => (int) 6,
	'has_pan_genomes' => false
)
$gene_selection = array(
	'parameters' => array(),
	'genes' => array()
)
$all_species = array(
	'ata' => array(
		'species' => 'ata',
		'common_name' => 'Aegilops tauschii',
		'tax_id' => '37682',
		'version' => 'Aet V4.0'
	),
	'asa' => array(
		'species' => 'asa',
		'common_name' => 'Allium sativum',
		'tax_id' => '4682',
		'version' => 'V1.0'
	),
	'atr' => array(
		'species' => 'atr',
		'common_name' => 'Amborella trichopoda',
		'tax_id' => '13333',
		'version' => 'JGI v1.0'
	),
	'aco' => array(
		'species' => 'aco',
		'common_name' => 'Ananas comosus',
		'tax_id' => '4615',
		'version' => 'JGI v3.0'
	),
	'aag' => array(
		'species' => 'aag',
		'common_name' => 'Anthoceros agrestis',
		'tax_id' => '41834',
		'version' => 'v1.1'
	),
	'ath' => array(
		'species' => 'ath',
		'common_name' => 'Arabidopsis thaliana',
		'tax_id' => '3702',
		'version' => 'Araport11'
	),
	'aof' => array(
		'species' => 'aof',
		'common_name' => 'Asparagus officinalis',
		'tax_id' => '4686',
		'version' => 'v1.1'
	),
	'bdi' => array(
		'species' => 'bdi',
		'common_name' => 'Brachypodium distachyon',
		'tax_id' => '15368',
		'version' => 'JGI v3.2'
	),
	'calsi' => array(
		'species' => 'calsi',
		'common_name' => 'Calamus simplicifolius',
		'tax_id' => '746888',
		'version' => 'v1.0'
	),
	'cpu' => array(
		'species' => 'cpu',
		'common_name' => 'Cenchrus purpureus',
		'tax_id' => '154765',
		'version' => 'v1.0'
	),
	'cde' => array(
		'species' => 'cde',
		'common_name' => 'Ceratophyllum demersum',
		'tax_id' => '4428',
		'version' => 'v1.0'
	),
	'cbr' => array(
		'species' => 'cbr',
		'common_name' => 'Chara braunii',
		'tax_id' => '69332',
		'version' => 'Cbr1.0'
	),
	'cre' => array(
		'species' => 'cre',
		'common_name' => 'Chlamydomonas reinhardtii',
		'tax_id' => '3055',
		'version' => 'JGI v5.5'
	),
	'dex' => array(
		'species' => 'dex',
		'common_name' => 'Digitaria exilis',
		'tax_id' => '1010633',
		'version' => 'Dexi_CM05836 v1'
	),
	'ddu' => array(
		'species' => 'ddu',
		'common_name' => 'Dioscorea dumetorum',
		'tax_id' => '167584',
		'version' => 'Trifoliate Yam v1.0'
	),
	'egu' => array(
		'species' => 'egu',
		'common_name' => 'Elaeis guineensis',
		'tax_id' => '51953',
		'version' => 'EG5.1'
	),
	'ecu' => array(
		'species' => 'ecu',
		'common_name' => 'Eragrostis curvula',
		'tax_id' => '38414',
		'version' => 'CERZOS_E.curvula1.0'
	),
	'gma' => array(
		'species' => 'gma',
		'common_name' => 'Glycine max',
		'tax_id' => '3847',
		'version' => 'JGI Wm82.a4.v1'
	),
	'hvu' => array(
		'species' => 'hvu',
		'common_name' => 'Hordeum vulgare',
		'tax_id' => '4513',
		'version' => 'Morex v2'
	),
	'lpe' => array(
		'species' => 'lpe',
		'common_name' => 'Lolium perenne',
		'tax_id' => '4522',
		'version' => '2.6.1-v3'
	),
	'mbi' => array(
		'species' => 'mbi',
		'common_name' => 'Magnolia biondii',
		'tax_id' => '86725',
		'version' => 'v1.0'
	),
	'mpo' => array(
		'species' => 'mpo',
		'common_name' => 'Marchantia polymorpha',
		'tax_id' => '3197',
		'version' => 'JGI v3.1'
	),
	'mco' => array(
		'species' => 'mco',
		'common_name' => 'Micromonas commoda',
		'tax_id' => '296587',
		'version' => 'JGI v3.0'
	),
	'msi' => array(
		'species' => 'msi',
		'common_name' => 'Miscanthus sinensis',
		'tax_id' => '62337',
		'version' => 'v7.1'
	),
	'mac' => array(
		'species' => 'mac',
		'common_name' => 'Musa acuminata',
		'tax_id' => '4641',
		'version' => 'Banana Genome v2.0'
	),
	'oth' => array(
		'species' => 'oth',
		'common_name' => 'Oropetium thomaeum',
		'tax_id' => '1148796',
		'version' => 'COGE v2.0'
	),
	'oal' => array(
		'species' => 'oal',
		'common_name' => 'Oryza alta',
		'tax_id' => '52545',
		'version' => 'OAv1'
	),
	'obr' => array(
		'species' => 'obr',
		'common_name' => 'Oryza brachyantha',
		'tax_id' => '4533',
		'version' => 'Ensembl Plants v1.4b'
	),
	'osak' => array(
		'species' => 'osak',
		'common_name' => 'Oryza sativa Kitaake',
		'tax_id' => '4530',
		'version' => 'V3.2'
	),
	'osaindica' => array(
		'species' => 'osaindica',
		'common_name' => 'Oryza sativa ssp. indica',
		'tax_id' => '39946',
		'version' => 'MBKBASE v1.0'
	),
	'osa' => array(
		'species' => 'osa',
		'common_name' => 'Oryza sativa ssp. japonica',
		'tax_id' => '39947',
		'version' => 'IRGSP-1.0-2021-05-10'
	),
	'pha' => array(
		'species' => 'pha',
		'common_name' => 'Panicum hallii',
		'tax_id' => '206008',
		'version' => 'JGI v3.2'
	),
	'ped' => array(
		'species' => 'ped',
		'common_name' => 'Phyllostachys edulis',
		'tax_id' => '38705',
		'version' => 'GigaDBv2.0'
	),
	'ppa' => array(
		'species' => 'ppa',
		'common_name' => 'Physcomitrium patens',
		'tax_id' => '3218',
		'version' => 'JGI v3.3'
	),
	'ptr' => array(
		'species' => 'ptr',
		'common_name' => 'Populus trichocarpa',
		'tax_id' => '3694',
		'version' => 'JGI v4.1'
	),
	'pco' => array(
		'species' => 'pco',
		'common_name' => 'Prasinoderma coloniale',
		'tax_id' => '156133',
		'version' => 'v1.0'
	),
	'ssp' => array(
		'species' => 'ssp',
		'common_name' => 'Saccharum spontaneum',
		'tax_id' => '62335',
		'version' => 'v20190103'
	),
	'sce' => array(
		'species' => 'sce',
		'common_name' => 'Secale cereale',
		'tax_id' => '4550',
		'version' => 'Rye v1.0'
	),
	'smo' => array(
		'species' => 'smo',
		'common_name' => 'Selaginella moellendorffii',
		'tax_id' => '88036',
		'version' => 'v1.0'
	),
	'sgi' => array(
		'species' => 'sgi',
		'common_name' => 'Sequoiadendron giganteum',
		'tax_id' => '99814',
		'version' => 'V2.0'
	),
	'sit' => array(
		'species' => 'sit',
		'common_name' => 'Setaria italica',
		'tax_id' => '4555',
		'version' => 'JGI v2.2'
	),
	'svi' => array(
		'species' => 'svi',
		'common_name' => 'Setaria viridis',
		'tax_id' => '4556',
		'version' => 'Phytozome v2.1'
	),
	'sly' => array(
		'species' => 'sly',
		'common_name' => 'Solanum lycopersicum',
		'tax_id' => '4081',
		'version' => 'ITAG4.0'
	),
	'sbi' => array(
		'species' => 'sbi',
		'common_name' => 'Sorghum bicolor',
		'tax_id' => '4558',
		'version' => 'JGI v3.1'
	),
	'spo' => array(
		'species' => 'spo',
		'common_name' => 'Spirodela polyrhiza',
		'tax_id' => '29656',
		'version' => 'JGI v2.0'
	),
	'tae' => array(
		'species' => 'tae',
		'common_name' => 'Triticum aestivum',
		'tax_id' => '4565',
		'version' => 'IWGSCv2.1'
	),
	'tdi' => array(
		'species' => 'tdi',
		'common_name' => 'Triticum dicoccoides',
		'tax_id' => '85692',
		'version' => 'Ensembl'
	),
	'ttu' => array(
		'species' => 'ttu',
		'common_name' => 'Triticum turgidum',
		'tax_id' => '4567',
		'version' => 'v1.0'
	),
	'vpl' => array(
		'species' => 'vpl',
		'common_name' => 'Vanilla planifolia',
		'tax_id' => '51239',
		'version' => 'Elo Vpla-A Principal v1.0'
	),
	'zma' => array(
		'species' => 'zma',
		'common_name' => 'Zea mays B73',
		'tax_id' => '4577',
		'version' => 'NAM v5.0'
	),
	'zma-b104' => array(
		'species' => 'zma-b104',
		'common_name' => 'Zea mays B104',
		'tax_id' => '4577',
		'version' => 'v1.0'
	),
	'zosmarina' => array(
		'species' => 'zosmarina',
		'common_name' => 'Zostera marina',
		'tax_id' => '29655',
		'version' => 'v3.1'
	),
	'zjn' => array(
		'species' => 'zjn',
		'common_name' => 'Zoysia japonica ssp. nagirizaki',
		'tax_id' => '309978',
		'version' => 'Zoysia Genome Database v1.1'
	)
)
$subfamily_family_types = array(
	(int) 0 => 'ORTHOFAM'
)
$parental_family_types = array(
	(int) 0 => 'HOMFAM'
)
$gene_family_types_information = array(
	'HOMFAM' => array(
		'id' => 'HOMFAM',
		'name' => 'Homologous gene family',
		'gene_type' => 'coding',
		'parent_id' => '',
		'ancestry' => 'homology'
	),
	'ORTHOFAM' => array(
		'id' => 'ORTHOFAM',
		'name' => 'Orthologous gene family',
		'gene_type' => 'coding',
		'parent_id' => 'HOMFAM',
		'ancestry' => 'orthology'
	)
)
$allowed_data_types = array(
	'GO' => 'Gene Ontology',
	'INTERPRO' => 'InterPro',
	'GENE_FAMILY' => 'Gene Family'
)
$data_identifier_value = ''
$data_identifier_description = ''
$adt_title = 'Gene Family'
$adt = 'GENE_FAMILY'
$is_selected = null
include - APP/View/Tools/similarity_heatmap.ctp, line 77
View::_evaluate() - CORE/Cake/View/View.php, line 971
View::_render() - CORE/Cake/View/View.php, line 933
View::render() - CORE/Cake/View/View.php, line 473
Controller::render() - CORE/Cake/Controller/Controller.php, line 963
Dispatcher::_invoke() - CORE/Cake/Routing/Dispatcher.php, line 200
Dispatcher::dispatch() - CORE/Cake/Routing/Dispatcher.php, line 167
[main] - APP/webroot/index.php, line 149

Warning (2): Invalid argument supplied for foreach() [APP/View/Tools/similarity_heatmap.ctp, line 77]
Code Context
                    <label>Source(s)</label>

                    <select class='form form-select' name='ontology_source_group' id='ontology_source_group'>

                        <?php foreach ($source_groups_information['available'] as $source_group_id) : ?>
$viewFile = '/www/bioinformatics01_ro/plaza/instances/monocots_05/app/View/Tools/similarity_heatmap.ctp'
$dataForView = array(
	'navigation_bar_info' => array(
		'num_colinearity_runs' => (int) 3,
		'num_colinearity_with_dating_runs' => (int) 2,
		'num_functional_clusters_runs' => (int) 6,
		'has_pan_genomes' => false
	),
	'gene_selection' => array(
		'parameters' => array(),
		'genes' => array()
	),
	'all_species' => array(
		'ata' => array(
			'species' => 'ata',
			'common_name' => 'Aegilops tauschii',
			'tax_id' => '37682',
			'version' => 'Aet V4.0'
		),
		'asa' => array(
			'species' => 'asa',
			'common_name' => 'Allium sativum',
			'tax_id' => '4682',
			'version' => 'V1.0'
		),
		'atr' => array(
			'species' => 'atr',
			'common_name' => 'Amborella trichopoda',
			'tax_id' => '13333',
			'version' => 'JGI v1.0'
		),
		'aco' => array(
			'species' => 'aco',
			'common_name' => 'Ananas comosus',
			'tax_id' => '4615',
			'version' => 'JGI v3.0'
		),
		'aag' => array(
			'species' => 'aag',
			'common_name' => 'Anthoceros agrestis',
			'tax_id' => '41834',
			'version' => 'v1.1'
		),
		'ath' => array(
			'species' => 'ath',
			'common_name' => 'Arabidopsis thaliana',
			'tax_id' => '3702',
			'version' => 'Araport11'
		),
		'aof' => array(
			'species' => 'aof',
			'common_name' => 'Asparagus officinalis',
			'tax_id' => '4686',
			'version' => 'v1.1'
		),
		'bdi' => array(
			'species' => 'bdi',
			'common_name' => 'Brachypodium distachyon',
			'tax_id' => '15368',
			'version' => 'JGI v3.2'
		),
		'calsi' => array(
			'species' => 'calsi',
			'common_name' => 'Calamus simplicifolius',
			'tax_id' => '746888',
			'version' => 'v1.0'
		),
		'cpu' => array(
			'species' => 'cpu',
			'common_name' => 'Cenchrus purpureus',
			'tax_id' => '154765',
			'version' => 'v1.0'
		),
		'cde' => array(
			'species' => 'cde',
			'common_name' => 'Ceratophyllum demersum',
			'tax_id' => '4428',
			'version' => 'v1.0'
		),
		'cbr' => array(
			'species' => 'cbr',
			'common_name' => 'Chara braunii',
			'tax_id' => '69332',
			'version' => 'Cbr1.0'
		),
		'cre' => array(
			'species' => 'cre',
			'common_name' => 'Chlamydomonas reinhardtii',
			'tax_id' => '3055',
			'version' => 'JGI v5.5'
		),
		'dex' => array(
			'species' => 'dex',
			'common_name' => 'Digitaria exilis',
			'tax_id' => '1010633',
			'version' => 'Dexi_CM05836 v1'
		),
		'ddu' => array(
			'species' => 'ddu',
			'common_name' => 'Dioscorea dumetorum',
			'tax_id' => '167584',
			'version' => 'Trifoliate Yam v1.0'
		),
		'egu' => array(
			'species' => 'egu',
			'common_name' => 'Elaeis guineensis',
			'tax_id' => '51953',
			'version' => 'EG5.1'
		),
		'ecu' => array(
			'species' => 'ecu',
			'common_name' => 'Eragrostis curvula',
			'tax_id' => '38414',
			'version' => 'CERZOS_E.curvula1.0'
		),
		'gma' => array(
			'species' => 'gma',
			'common_name' => 'Glycine max',
			'tax_id' => '3847',
			'version' => 'JGI Wm82.a4.v1'
		),
		'hvu' => array(
			'species' => 'hvu',
			'common_name' => 'Hordeum vulgare',
			'tax_id' => '4513',
			'version' => 'Morex v2'
		),
		'lpe' => array(
			'species' => 'lpe',
			'common_name' => 'Lolium perenne',
			'tax_id' => '4522',
			'version' => '2.6.1-v3'
		),
		'mbi' => array(
			'species' => 'mbi',
			'common_name' => 'Magnolia biondii',
			'tax_id' => '86725',
			'version' => 'v1.0'
		),
		'mpo' => array(
			'species' => 'mpo',
			'common_name' => 'Marchantia polymorpha',
			'tax_id' => '3197',
			'version' => 'JGI v3.1'
		),
		'mco' => array(
			'species' => 'mco',
			'common_name' => 'Micromonas commoda',
			'tax_id' => '296587',
			'version' => 'JGI v3.0'
		),
		'msi' => array(
			'species' => 'msi',
			'common_name' => 'Miscanthus sinensis',
			'tax_id' => '62337',
			'version' => 'v7.1'
		),
		'mac' => array(
			'species' => 'mac',
			'common_name' => 'Musa acuminata',
			'tax_id' => '4641',
			'version' => 'Banana Genome v2.0'
		),
		'oth' => array(
			'species' => 'oth',
			'common_name' => 'Oropetium thomaeum',
			'tax_id' => '1148796',
			'version' => 'COGE v2.0'
		),
		'oal' => array(
			'species' => 'oal',
			'common_name' => 'Oryza alta',
			'tax_id' => '52545',
			'version' => 'OAv1'
		),
		'obr' => array(
			'species' => 'obr',
			'common_name' => 'Oryza brachyantha',
			'tax_id' => '4533',
			'version' => 'Ensembl Plants v1.4b'
		),
		'osak' => array(
			'species' => 'osak',
			'common_name' => 'Oryza sativa Kitaake',
			'tax_id' => '4530',
			'version' => 'V3.2'
		),
		'osaindica' => array(
			'species' => 'osaindica',
			'common_name' => 'Oryza sativa ssp. indica',
			'tax_id' => '39946',
			'version' => 'MBKBASE v1.0'
		),
		'osa' => array(
			'species' => 'osa',
			'common_name' => 'Oryza sativa ssp. japonica',
			'tax_id' => '39947',
			'version' => 'IRGSP-1.0-2021-05-10'
		),
		'pha' => array(
			'species' => 'pha',
			'common_name' => 'Panicum hallii',
			'tax_id' => '206008',
			'version' => 'JGI v3.2'
		),
		'ped' => array(
			'species' => 'ped',
			'common_name' => 'Phyllostachys edulis',
			'tax_id' => '38705',
			'version' => 'GigaDBv2.0'
		),
		'ppa' => array(
			'species' => 'ppa',
			'common_name' => 'Physcomitrium patens',
			'tax_id' => '3218',
			'version' => 'JGI v3.3'
		),
		'ptr' => array(
			'species' => 'ptr',
			'common_name' => 'Populus trichocarpa',
			'tax_id' => '3694',
			'version' => 'JGI v4.1'
		),
		'pco' => array(
			'species' => 'pco',
			'common_name' => 'Prasinoderma coloniale',
			'tax_id' => '156133',
			'version' => 'v1.0'
		),
		'ssp' => array(
			'species' => 'ssp',
			'common_name' => 'Saccharum spontaneum',
			'tax_id' => '62335',
			'version' => 'v20190103'
		),
		'sce' => array(
			'species' => 'sce',
			'common_name' => 'Secale cereale',
			'tax_id' => '4550',
			'version' => 'Rye v1.0'
		),
		'smo' => array(
			'species' => 'smo',
			'common_name' => 'Selaginella moellendorffii',
			'tax_id' => '88036',
			'version' => 'v1.0'
		),
		'sgi' => array(
			'species' => 'sgi',
			'common_name' => 'Sequoiadendron giganteum',
			'tax_id' => '99814',
			'version' => 'V2.0'
		),
		'sit' => array(
			'species' => 'sit',
			'common_name' => 'Setaria italica',
			'tax_id' => '4555',
			'version' => 'JGI v2.2'
		),
		'svi' => array(
			'species' => 'svi',
			'common_name' => 'Setaria viridis',
			'tax_id' => '4556',
			'version' => 'Phytozome v2.1'
		),
		'sly' => array(
			'species' => 'sly',
			'common_name' => 'Solanum lycopersicum',
			'tax_id' => '4081',
			'version' => 'ITAG4.0'
		),
		'sbi' => array(
			'species' => 'sbi',
			'common_name' => 'Sorghum bicolor',
			'tax_id' => '4558',
			'version' => 'JGI v3.1'
		),
		'spo' => array(
			'species' => 'spo',
			'common_name' => 'Spirodela polyrhiza',
			'tax_id' => '29656',
			'version' => 'JGI v2.0'
		),
		'tae' => array(
			'species' => 'tae',
			'common_name' => 'Triticum aestivum',
			'tax_id' => '4565',
			'version' => 'IWGSCv2.1'
		),
		'tdi' => array(
			'species' => 'tdi',
			'common_name' => 'Triticum dicoccoides',
			'tax_id' => '85692',
			'version' => 'Ensembl'
		),
		'ttu' => array(
			'species' => 'ttu',
			'common_name' => 'Triticum turgidum',
			'tax_id' => '4567',
			'version' => 'v1.0'
		),
		'vpl' => array(
			'species' => 'vpl',
			'common_name' => 'Vanilla planifolia',
			'tax_id' => '51239',
			'version' => 'Elo Vpla-A Principal v1.0'
		),
		'zma' => array(
			'species' => 'zma',
			'common_name' => 'Zea mays B73',
			'tax_id' => '4577',
			'version' => 'NAM v5.0'
		),
		'zma-b104' => array(
			'species' => 'zma-b104',
			'common_name' => 'Zea mays B104',
			'tax_id' => '4577',
			'version' => 'v1.0'
		),
		'zosmarina' => array(
			'species' => 'zosmarina',
			'common_name' => 'Zostera marina',
			'tax_id' => '29655',
			'version' => 'v3.1'
		),
		'zjn' => array(
			'species' => 'zjn',
			'common_name' => 'Zoysia japonica ssp. nagirizaki',
			'tax_id' => '309978',
			'version' => 'Zoysia Genome Database v1.1'
		)
	),
	'subfamily_family_types' => array(
		(int) 0 => 'ORTHOFAM'
	),
	'parental_family_types' => array(
		(int) 0 => 'HOMFAM'
	),
	'gene_family_types_information' => array(
		'HOMFAM' => array(
			'id' => 'HOMFAM',
			'name' => 'Homologous gene family',
			'gene_type' => 'coding',
			'parent_id' => '',
			'ancestry' => 'homology'
		),
		'ORTHOFAM' => array(
			'id' => 'ORTHOFAM',
			'name' => 'Orthologous gene family',
			'gene_type' => 'coding',
			'parent_id' => 'HOMFAM',
			'ancestry' => 'orthology'
		)
	),
	'allowed_data_types' => array(
		'GO' => 'Gene Ontology',
		'INTERPRO' => 'InterPro',
		'GENE_FAMILY' => 'Gene Family'
	)
)
$navigation_bar_info = array(
	'num_colinearity_runs' => (int) 3,
	'num_colinearity_with_dating_runs' => (int) 2,
	'num_functional_clusters_runs' => (int) 6,
	'has_pan_genomes' => false
)
$gene_selection = array(
	'parameters' => array(),
	'genes' => array()
)
$all_species = array(
	'ata' => array(
		'species' => 'ata',
		'common_name' => 'Aegilops tauschii',
		'tax_id' => '37682',
		'version' => 'Aet V4.0'
	),
	'asa' => array(
		'species' => 'asa',
		'common_name' => 'Allium sativum',
		'tax_id' => '4682',
		'version' => 'V1.0'
	),
	'atr' => array(
		'species' => 'atr',
		'common_name' => 'Amborella trichopoda',
		'tax_id' => '13333',
		'version' => 'JGI v1.0'
	),
	'aco' => array(
		'species' => 'aco',
		'common_name' => 'Ananas comosus',
		'tax_id' => '4615',
		'version' => 'JGI v3.0'
	),
	'aag' => array(
		'species' => 'aag',
		'common_name' => 'Anthoceros agrestis',
		'tax_id' => '41834',
		'version' => 'v1.1'
	),
	'ath' => array(
		'species' => 'ath',
		'common_name' => 'Arabidopsis thaliana',
		'tax_id' => '3702',
		'version' => 'Araport11'
	),
	'aof' => array(
		'species' => 'aof',
		'common_name' => 'Asparagus officinalis',
		'tax_id' => '4686',
		'version' => 'v1.1'
	),
	'bdi' => array(
		'species' => 'bdi',
		'common_name' => 'Brachypodium distachyon',
		'tax_id' => '15368',
		'version' => 'JGI v3.2'
	),
	'calsi' => array(
		'species' => 'calsi',
		'common_name' => 'Calamus simplicifolius',
		'tax_id' => '746888',
		'version' => 'v1.0'
	),
	'cpu' => array(
		'species' => 'cpu',
		'common_name' => 'Cenchrus purpureus',
		'tax_id' => '154765',
		'version' => 'v1.0'
	),
	'cde' => array(
		'species' => 'cde',
		'common_name' => 'Ceratophyllum demersum',
		'tax_id' => '4428',
		'version' => 'v1.0'
	),
	'cbr' => array(
		'species' => 'cbr',
		'common_name' => 'Chara braunii',
		'tax_id' => '69332',
		'version' => 'Cbr1.0'
	),
	'cre' => array(
		'species' => 'cre',
		'common_name' => 'Chlamydomonas reinhardtii',
		'tax_id' => '3055',
		'version' => 'JGI v5.5'
	),
	'dex' => array(
		'species' => 'dex',
		'common_name' => 'Digitaria exilis',
		'tax_id' => '1010633',
		'version' => 'Dexi_CM05836 v1'
	),
	'ddu' => array(
		'species' => 'ddu',
		'common_name' => 'Dioscorea dumetorum',
		'tax_id' => '167584',
		'version' => 'Trifoliate Yam v1.0'
	),
	'egu' => array(
		'species' => 'egu',
		'common_name' => 'Elaeis guineensis',
		'tax_id' => '51953',
		'version' => 'EG5.1'
	),
	'ecu' => array(
		'species' => 'ecu',
		'common_name' => 'Eragrostis curvula',
		'tax_id' => '38414',
		'version' => 'CERZOS_E.curvula1.0'
	),
	'gma' => array(
		'species' => 'gma',
		'common_name' => 'Glycine max',
		'tax_id' => '3847',
		'version' => 'JGI Wm82.a4.v1'
	),
	'hvu' => array(
		'species' => 'hvu',
		'common_name' => 'Hordeum vulgare',
		'tax_id' => '4513',
		'version' => 'Morex v2'
	),
	'lpe' => array(
		'species' => 'lpe',
		'common_name' => 'Lolium perenne',
		'tax_id' => '4522',
		'version' => '2.6.1-v3'
	),
	'mbi' => array(
		'species' => 'mbi',
		'common_name' => 'Magnolia biondii',
		'tax_id' => '86725',
		'version' => 'v1.0'
	),
	'mpo' => array(
		'species' => 'mpo',
		'common_name' => 'Marchantia polymorpha',
		'tax_id' => '3197',
		'version' => 'JGI v3.1'
	),
	'mco' => array(
		'species' => 'mco',
		'common_name' => 'Micromonas commoda',
		'tax_id' => '296587',
		'version' => 'JGI v3.0'
	),
	'msi' => array(
		'species' => 'msi',
		'common_name' => 'Miscanthus sinensis',
		'tax_id' => '62337',
		'version' => 'v7.1'
	),
	'mac' => array(
		'species' => 'mac',
		'common_name' => 'Musa acuminata',
		'tax_id' => '4641',
		'version' => 'Banana Genome v2.0'
	),
	'oth' => array(
		'species' => 'oth',
		'common_name' => 'Oropetium thomaeum',
		'tax_id' => '1148796',
		'version' => 'COGE v2.0'
	),
	'oal' => array(
		'species' => 'oal',
		'common_name' => 'Oryza alta',
		'tax_id' => '52545',
		'version' => 'OAv1'
	),
	'obr' => array(
		'species' => 'obr',
		'common_name' => 'Oryza brachyantha',
		'tax_id' => '4533',
		'version' => 'Ensembl Plants v1.4b'
	),
	'osak' => array(
		'species' => 'osak',
		'common_name' => 'Oryza sativa Kitaake',
		'tax_id' => '4530',
		'version' => 'V3.2'
	),
	'osaindica' => array(
		'species' => 'osaindica',
		'common_name' => 'Oryza sativa ssp. indica',
		'tax_id' => '39946',
		'version' => 'MBKBASE v1.0'
	),
	'osa' => array(
		'species' => 'osa',
		'common_name' => 'Oryza sativa ssp. japonica',
		'tax_id' => '39947',
		'version' => 'IRGSP-1.0-2021-05-10'
	),
	'pha' => array(
		'species' => 'pha',
		'common_name' => 'Panicum hallii',
		'tax_id' => '206008',
		'version' => 'JGI v3.2'
	),
	'ped' => array(
		'species' => 'ped',
		'common_name' => 'Phyllostachys edulis',
		'tax_id' => '38705',
		'version' => 'GigaDBv2.0'
	),
	'ppa' => array(
		'species' => 'ppa',
		'common_name' => 'Physcomitrium patens',
		'tax_id' => '3218',
		'version' => 'JGI v3.3'
	),
	'ptr' => array(
		'species' => 'ptr',
		'common_name' => 'Populus trichocarpa',
		'tax_id' => '3694',
		'version' => 'JGI v4.1'
	),
	'pco' => array(
		'species' => 'pco',
		'common_name' => 'Prasinoderma coloniale',
		'tax_id' => '156133',
		'version' => 'v1.0'
	),
	'ssp' => array(
		'species' => 'ssp',
		'common_name' => 'Saccharum spontaneum',
		'tax_id' => '62335',
		'version' => 'v20190103'
	),
	'sce' => array(
		'species' => 'sce',
		'common_name' => 'Secale cereale',
		'tax_id' => '4550',
		'version' => 'Rye v1.0'
	),
	'smo' => array(
		'species' => 'smo',
		'common_name' => 'Selaginella moellendorffii',
		'tax_id' => '88036',
		'version' => 'v1.0'
	),
	'sgi' => array(
		'species' => 'sgi',
		'common_name' => 'Sequoiadendron giganteum',
		'tax_id' => '99814',
		'version' => 'V2.0'
	),
	'sit' => array(
		'species' => 'sit',
		'common_name' => 'Setaria italica',
		'tax_id' => '4555',
		'version' => 'JGI v2.2'
	),
	'svi' => array(
		'species' => 'svi',
		'common_name' => 'Setaria viridis',
		'tax_id' => '4556',
		'version' => 'Phytozome v2.1'
	),
	'sly' => array(
		'species' => 'sly',
		'common_name' => 'Solanum lycopersicum',
		'tax_id' => '4081',
		'version' => 'ITAG4.0'
	),
	'sbi' => array(
		'species' => 'sbi',
		'common_name' => 'Sorghum bicolor',
		'tax_id' => '4558',
		'version' => 'JGI v3.1'
	),
	'spo' => array(
		'species' => 'spo',
		'common_name' => 'Spirodela polyrhiza',
		'tax_id' => '29656',
		'version' => 'JGI v2.0'
	),
	'tae' => array(
		'species' => 'tae',
		'common_name' => 'Triticum aestivum',
		'tax_id' => '4565',
		'version' => 'IWGSCv2.1'
	),
	'tdi' => array(
		'species' => 'tdi',
		'common_name' => 'Triticum dicoccoides',
		'tax_id' => '85692',
		'version' => 'Ensembl'
	),
	'ttu' => array(
		'species' => 'ttu',
		'common_name' => 'Triticum turgidum',
		'tax_id' => '4567',
		'version' => 'v1.0'
	),
	'vpl' => array(
		'species' => 'vpl',
		'common_name' => 'Vanilla planifolia',
		'tax_id' => '51239',
		'version' => 'Elo Vpla-A Principal v1.0'
	),
	'zma' => array(
		'species' => 'zma',
		'common_name' => 'Zea mays B73',
		'tax_id' => '4577',
		'version' => 'NAM v5.0'
	),
	'zma-b104' => array(
		'species' => 'zma-b104',
		'common_name' => 'Zea mays B104',
		'tax_id' => '4577',
		'version' => 'v1.0'
	),
	'zosmarina' => array(
		'species' => 'zosmarina',
		'common_name' => 'Zostera marina',
		'tax_id' => '29655',
		'version' => 'v3.1'
	),
	'zjn' => array(
		'species' => 'zjn',
		'common_name' => 'Zoysia japonica ssp. nagirizaki',
		'tax_id' => '309978',
		'version' => 'Zoysia Genome Database v1.1'
	)
)
$subfamily_family_types = array(
	(int) 0 => 'ORTHOFAM'
)
$parental_family_types = array(
	(int) 0 => 'HOMFAM'
)
$gene_family_types_information = array(
	'HOMFAM' => array(
		'id' => 'HOMFAM',
		'name' => 'Homologous gene family',
		'gene_type' => 'coding',
		'parent_id' => '',
		'ancestry' => 'homology'
	),
	'ORTHOFAM' => array(
		'id' => 'ORTHOFAM',
		'name' => 'Orthologous gene family',
		'gene_type' => 'coding',
		'parent_id' => 'HOMFAM',
		'ancestry' => 'orthology'
	)
)
$allowed_data_types = array(
	'GO' => 'Gene Ontology',
	'INTERPRO' => 'InterPro',
	'GENE_FAMILY' => 'Gene Family'
)
$data_identifier_value = ''
$data_identifier_description = ''
$adt_title = 'Gene Family'
$adt = 'GENE_FAMILY'
$is_selected = null
include - APP/View/Tools/similarity_heatmap.ctp, line 77
View::_evaluate() - CORE/Cake/View/View.php, line 971
View::_render() - CORE/Cake/View/View.php, line 933
View::render() - CORE/Cake/View/View.php, line 473
Controller::render() - CORE/Cake/Controller/Controller.php, line 963
Dispatcher::_invoke() - CORE/Cake/Routing/Dispatcher.php, line 200
Dispatcher::dispatch() - CORE/Cake/Routing/Dispatcher.php, line 167
[main] - APP/webroot/index.php, line 149