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Bugfix/make the inferred cell type options dynamic shown or disabled in marker gene heatmap dropdown menu #482

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Bugfix/make the inferred cell type options dynamic shown or disabled in marker gene heatmap dropdown menu #482

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8e7177a
Fetch marker gene id with experiment accession from the DB
upendrakumbham Oct 21, 2024
9b74beb
Merge branch 'develop' into make-the-inferred-cell-type-options-dynam…
upendrakumbham Oct 21, 2024
4ab3665
Fix broken tests
upendrakumbham Oct 24, 2024
2e3cb5d
Update SQL query
upendrakumbham Oct 24, 2024
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7 changes: 6 additions & 1 deletion app/src/main/java/uk/ac/ebi/atlas/experimentpage/markergenes/MarkerGeneService.java
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Original file line number Diff line number Diff line change
@@ -1,6 +1,5 @@
package uk.ac.ebi.atlas.experimentpage.markergenes;

import com.google.common.collect.ImmutableCollection;
import com.google.common.collect.ImmutableList;
import com.google.common.collect.ImmutableSet;
import org.springframework.stereotype.Service;
Expand Down Expand Up @@ -64,6 +63,7 @@ public ImmutableList<MarkerGene> getCellTypeMarkerGeneHeatmapData(String experim
.filter(markerGene -> !markerGene.cellGroupValueWhereMarker().equalsIgnoreCase("Not available"))
.collect(toImmutableList());
}

/**
* @param experimentAccession - Id of the experiment
* @param k - no of clusters
Expand All @@ -73,4 +73,9 @@ public ImmutableList<MarkerGene> getCellTypeMarkerGeneHeatmapData(String experim
public ImmutableList<MarkerGene> getMarkerGenesPerCluster(String experimentAccession, String k) {
return ImmutableList.copyOf(markerGenesDao.getMarkerGenesWithAveragesPerCluster(experimentAccession, k));
}

public Integer isMarkerGenesAvailableForTheInferredCellTypes(String experimentAccession, String cellGroupType) {
return markerGenesDao.getMarkerGenesForTheInferredCellTypes(experimentAccession, cellGroupType);
}

}
162 changes: 94 additions & 68 deletions app/src/main/java/uk/ac/ebi/atlas/experimentpage/markergenes/MarkerGenesDao.java
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Original file line number Diff line number Diff line change
Expand Up @@ -9,14 +9,8 @@

@Repository
public class MarkerGenesDao {
private final NamedParameterJdbcTemplate namedParameterJdbcTemplate;
static final String CELL_TYPE_ONTOLOGY_LABELS = "inferred cell type - ontology labels";
static final String CELL_TYPE_AUTHOR_LABELS = "inferred cell type - authors labels";

public MarkerGenesDao(NamedParameterJdbcTemplate namedParameterJdbcTemplate) {
this.namedParameterJdbcTemplate = namedParameterJdbcTemplate;
}

private static final String SELECT_MARKER_GENES_WITH_AVERAGES_PER_CLUSTER =
"SELECT " +
"g.experiment_accession, " +
Expand All @@ -28,13 +22,13 @@ public MarkerGenesDao(NamedParameterJdbcTemplate namedParameterJdbcTemplate) {
"s.mean_expression, " +
"s.median_expression, " +
"e.expression_unit " +
"FROM " +
"FROM " +
"scxa_cell_group_marker_gene_stats s, " +
"scxa_cell_group_marker_genes m, " +
"scxa_cell_group g, " +
"scxa_cell_group h, " +
"experiment e " +
"WHERE " +
"WHERE " +
"s.cell_group_id = g.id AND " +
"s.marker_id = m.id AND " +
"m.cell_group_id = h.id AND " +
Expand All @@ -43,44 +37,16 @@ public MarkerGenesDao(NamedParameterJdbcTemplate namedParameterJdbcTemplate) {
"g.variable = :k AND " +
"s.expression_type = 0 AND " +
"e.accession = g.experiment_accession " +
"ORDER BY " +
"ORDER BY " +
"m.marker_probability";

public List<MarkerGene> getMarkerGenesWithAveragesPerCluster(String experimentAccession, String k) {
var namedParameters =
ImmutableMap.of(
"experiment_accession", experimentAccession,
"k", k);

return namedParameterJdbcTemplate.query(
SELECT_MARKER_GENES_WITH_AVERAGES_PER_CLUSTER,
namedParameters,
(resultSet, rowNumber) -> MarkerGene.create(
resultSet.getString("gene_id"),
resultSet.getString("k_where_marker"),
resultSet.getString("cluster_id_where_marker"),
resultSet.getDouble("marker_p_value"),
resultSet.getString("cluster_id"),
resultSet.getDouble("median_expression"),
resultSet.getDouble("mean_expression"),
resultSet.getString("expression_unit")));
}

private static final String SELECT_DISTINCT_KS_WITH_MARKER_GENES =
"SELECT DISTINCT h.variable as k_where_marker " +
"FROM scxa_cell_group_marker_genes m, scxa_cell_group h " +
"WHERE m.cell_group_id = h.id AND " +
"h.experiment_accession = :experiment_accession AND m.marker_probability < 0.05 " +
"ORDER BY k_where_marker ASC";

public List<String> getKsWithMarkerGenes(String experimentAccession) {
var namedParameters = ImmutableMap.of("experiment_accession", experimentAccession);
return namedParameterJdbcTemplate.queryForList(
SELECT_DISTINCT_KS_WITH_MARKER_GENES,
namedParameters,
String.class);
}

private static final String SELECT_MARKER_GENES_WITH_AVERAGES_PER_CELL_GROUP =
"SELECT " +
"g.experiment_accession, " +
Expand All @@ -92,13 +58,13 @@ public List<String> getKsWithMarkerGenes(String experimentAccession) {
"s.mean_expression, " +
"s.median_expression, " +
"e.expression_unit " +
"FROM " +
"FROM " +
"scxa_cell_group_marker_gene_stats s, " +
"scxa_cell_group_marker_genes m, " +
"scxa_cell_group g, " +
"scxa_cell_group h, " +
"experiment e " +
"WHERE " +
"WHERE " +
"s.cell_group_id = g.id AND " +
"s.marker_id = m.id AND " +
"m.cell_group_id = h.id AND " +
Expand All @@ -108,9 +74,84 @@ public List<String> getKsWithMarkerGenes(String experimentAccession) {
"g.value IN (:values) AND " +
"s.expression_type = 0 AND " +
"e.accession = g.experiment_accession " +
"ORDER BY " +
"ORDER BY " +
"m.marker_probability ";

private static final String SELECT_MARKER_GENES_WITH_AVERAGES_PER_CELL_GROUP_ALL =
"SELECT " +
"g.experiment_accession, " +
"m.gene_id, " +
"g.variable AS cell_group_type, " +
"h.value AS cell_group_value_where_marker, " +
"g.value AS cell_group_value, " +
"m.marker_probability AS marker_p_value, " +
"s.mean_expression, " +
"s.median_expression, " +
"e.expression_unit " +
"FROM " +
"scxa_cell_group_marker_gene_stats s, " +
"scxa_cell_group_marker_genes m, " +
"scxa_cell_group g, " +
"scxa_cell_group h, " +
"experiment e " +
"WHERE " +
"s.cell_group_id = g.id AND " +
"s.marker_id = m.id AND " +
"m.cell_group_id = h.id AND " +
"g.experiment_accession = :experiment_accession AND " +
"m.marker_probability < 0.05 AND " +
"g.variable = :variable AND " +
"s.expression_type = 0 AND " +
"e.accession = g.experiment_accession " +
"ORDER BY " +
"m.marker_probability ";

private static final String SELECT_MARKER_GENES_FOR_INFERRED_CELL_TYPES =
"SELECT count(m.gene_id) as marker_genes " +
"FROM " +
"scxa_cell_group_marker_genes m, " +
"scxa_cell_group h " +
"WHERE " +
"m.cell_group_id = h.id AND " +
"h.experiment_accession = :experiment_accession AND " +
"m.marker_probability < 0.05 AND " +
"h.variable= :variable " +
"LIMIT 1";

private final NamedParameterJdbcTemplate namedParameterJdbcTemplate;

public MarkerGenesDao(NamedParameterJdbcTemplate namedParameterJdbcTemplate) {
this.namedParameterJdbcTemplate = namedParameterJdbcTemplate;
}

public List<MarkerGene> getMarkerGenesWithAveragesPerCluster(String experimentAccession, String k) {
var namedParameters =
ImmutableMap.of(
"experiment_accession", experimentAccession,
"k", k);

return namedParameterJdbcTemplate.query(
SELECT_MARKER_GENES_WITH_AVERAGES_PER_CLUSTER,
namedParameters,
(resultSet, rowNumber) -> MarkerGene.create(
resultSet.getString("gene_id"),
resultSet.getString("k_where_marker"),
resultSet.getString("cluster_id_where_marker"),
resultSet.getDouble("marker_p_value"),
resultSet.getString("cluster_id"),
resultSet.getDouble("median_expression"),
resultSet.getDouble("mean_expression"),
resultSet.getString("expression_unit")));
}

public List<String> getKsWithMarkerGenes(String experimentAccession) {
var namedParameters = ImmutableMap.of("experiment_accession", experimentAccession);
return namedParameterJdbcTemplate.queryForList(
SELECT_DISTINCT_KS_WITH_MARKER_GENES,
namedParameters,
String.class);
}

public List<MarkerGene> getCellTypeMarkerGenesOntologyLabels(String experimentAccession,
ImmutableCollection<String> cellGroupValues) {
return getCellTypeMarkerGenes(experimentAccession, CELL_TYPE_ONTOLOGY_LABELS, cellGroupValues);
Expand Down Expand Up @@ -148,34 +189,6 @@ public List<MarkerGene> getCellTypeMarkerGenes(String experiment_accession,
resultSet.getString("expression_unit")));
}

private static final String SELECT_MARKER_GENES_WITH_AVERAGES_PER_CELL_GROUP_ALL =
"SELECT " +
"g.experiment_accession, " +
"m.gene_id, " +
"g.variable AS cell_group_type, " +
"h.value AS cell_group_value_where_marker, " +
"g.value AS cell_group_value, " +
"m.marker_probability AS marker_p_value, " +
"s.mean_expression, " +
"s.median_expression, " +
"e.expression_unit " +
"FROM " +
"scxa_cell_group_marker_gene_stats s, " +
"scxa_cell_group_marker_genes m, " +
"scxa_cell_group g, " +
"scxa_cell_group h, " +
"experiment e " +
"WHERE " +
"s.cell_group_id = g.id AND " +
"s.marker_id = m.id AND " +
"m.cell_group_id = h.id AND " +
"g.experiment_accession = :experiment_accession AND " +
"m.marker_probability < 0.05 AND " +
"g.variable = :variable AND " +
"s.expression_type = 0 AND " +
"e.accession = g.experiment_accession " +
"ORDER BY " +
"m.marker_probability ";
public List<MarkerGene> getCellTypeMarkerGenes(String experiment_accession,
String cellTypeVariable) {
var namedParameters =
Expand All @@ -196,4 +209,17 @@ public List<MarkerGene> getCellTypeMarkerGenes(String experiment_accession,
resultSet.getDouble("mean_expression"),
resultSet.getString("expression_unit")));
}

public Integer getMarkerGenesForTheInferredCellTypes(String experimentAccession, String cellGroupType) {
var namedParameters =
ImmutableMap.of(
"experiment_accession", experimentAccession,
"variable", cellGroupType);

return namedParameterJdbcTemplate.queryForObject(
SELECT_MARKER_GENES_FOR_INFERRED_CELL_TYPES,
namedParameters,
Integer.class);

}
}
8 changes: 7 additions & 1 deletion app/src/main/java/uk/ac/ebi/atlas/experimentpage/tabs/ExperimentPageContentService.java
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Original file line number Diff line number Diff line change
Expand Up @@ -13,6 +13,7 @@
import uk.ac.ebi.atlas.download.ExperimentFileType;
import uk.ac.ebi.atlas.experimentpage.ExternallyAvailableContentService;
import uk.ac.ebi.atlas.experimentpage.cellplot.CellPlotService;
import uk.ac.ebi.atlas.experimentpage.markergenes.MarkerGeneService;
import uk.ac.ebi.atlas.experimentpage.metadata.CellMetadataService;
import uk.ac.ebi.atlas.experimentpage.tsneplot.TSnePlotSettingsService;
import uk.ac.ebi.atlas.model.download.ExternallyAvailableContent;
Expand All @@ -36,6 +37,7 @@ public class ExperimentPageContentService {
private final OntologyAccessionsSearchService ontologyAccessionsSearchService;
private final ExperimentTrader experimentTrader;
private final CellPlotService cellPlotService;
private final MarkerGeneService markerGeneService;

final static ImmutableSet<String> EXPERIMENTS_WITH_NO_ANATOMOGRAM = ImmutableSet.of(
"E-CURD-10", "E-CURD-11", "E-CURD-126", "E-CURD-135",
Expand All @@ -50,14 +52,15 @@ public ExperimentPageContentService(ExperimentFileLocationService experimentFile
CellMetadataService cellMetadataService,
OntologyAccessionsSearchService ontologyAccessionsSearchService,
ExperimentTrader experimentTrader,
CellPlotService cellPlotService) {
CellPlotService cellPlotService, MarkerGeneService markerGeneService) {
this.experimentFileLocationService = experimentFileLocationService;
this.dataFileHub = dataFileHub;
this.tsnePlotSettingsService = tsnePlotSettingsService;
this.cellMetadataService = cellMetadataService;
this.ontologyAccessionsSearchService = ontologyAccessionsSearchService;
this.experimentTrader = experimentTrader;
this.cellPlotService = cellPlotService;
this.markerGeneService = markerGeneService;
}

public JsonObject getTsnePlotData(String experimentAccession) {
Expand All @@ -81,6 +84,9 @@ public JsonObject getTsnePlotData(String experimentAccession) {
GSON.toJsonTree(fetchDefaultPlotMethodAndParameterisation(experimentAccession)));

result.add("metadata", getMetadata(experimentAccession));
result.add("markerGeneMetadata", GSON.toJsonTree
(markerGeneService.isMarkerGenesAvailableForTheInferredCellTypes(experimentAccession,
"inferred cell type - ontology labels")));

var units = new JsonArray();
units.add("CPM");
Expand Down
7 changes: 6 additions & 1 deletion app/src/test/java/uk/ac/ebi/atlas/experimentpage/tabs/ExperimentPageContentServiceIT.java
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Original file line number Diff line number Diff line change
Expand Up @@ -17,6 +17,7 @@
import uk.ac.ebi.atlas.configuration.TestConfig;
import uk.ac.ebi.atlas.download.ExperimentFileLocationService;
import uk.ac.ebi.atlas.experimentpage.cellplot.CellPlotService;
import uk.ac.ebi.atlas.experimentpage.markergenes.MarkerGeneService;
import uk.ac.ebi.atlas.experimentpage.tsneplot.TSnePlotSettingsService;
import uk.ac.ebi.atlas.experimentpage.metadata.CellMetadataService;
import uk.ac.ebi.atlas.resource.DataFileHub;
Expand Down Expand Up @@ -62,6 +63,9 @@ class ExperimentPageContentServiceIT {
@Inject
private CellPlotService cellPlotService;

@Inject
private MarkerGeneService markerGeneService;

private ExperimentPageContentService subject;

@BeforeAll
Expand Down Expand Up @@ -101,7 +105,8 @@ void setUp() {
cellMetadataService,
ontologyAccessionsSearchService,
experimentTrader,
cellPlotService);
cellPlotService,
markerGeneService);
}

@Test
Expand Down
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