gene set summary progress (#2127)

* revert removal of cache control headers * checkpoint work on revising summary route * add summary query support to annoMatrix * summarize route cleanup * add mising file * clean up summarize route * add summary histogram * update deps * lint * more lint * lint * manage crossfiler during gene set state changes * remove obsolete debugging code * correctly perform async watch in histogram * better error handling
2026-10-07 17:58:11 +08:00 · 2021-03-30 14:43:53 -07:00
parent bfb9e1edcc
commit ae30b66123
47 changed files with 28628 additions and 9109 deletions
@@ -0,0 +1,126 @@
+/*
+Action creators for gene sets
+
+Primarily used to keep the crossfilter and underlying data in sync with the UI.
+
+The behavior manifest in these action creators:
+
+    Delete a gene set, will
+      * drop index & clear selection state on the gene set summary
+      * drop index & clear selection state of each gene in the geneset
+
+    Delete a gene from a gene set, will:
+      * drop index & clear selection state on the gene set summary
+      * drop index & clear selection state on the gene
+
+    Add a gene to a gene set, will:
+      * drop index & clear selection state on the gene set summary
+      * will NOT touch the selection state for the gene
+  
+Note that crossfilter indices are lazy created, as needed.
+*/
+
+export const genesetDelete = (genesetName) => (dispatch, getState) => {
+  const state = getState();
+  const { genesets } = state;
+  const gs = genesets?.genesets?.get(genesetName) ?? {};
+  const geneSymbols = Array.from(gs.genes.keys());
+  const obsCrossfilter = dropGeneset(dispatch, state, genesetName, geneSymbols);
+  dispatch({
+    type: "geneset: delete",
+    genesetName,
+    obsCrossfilter,
+    annoMatrix: obsCrossfilter.annoMatrix,
+  });
+};
+
+export const genesetAddGenes = (genesetName, genes) => (dispatch, getState) => {
+  const state = getState();
+  const { obsCrossfilter: prevObsCrossfilter } = state;
+  const obsCrossfilter = dropGenesetSummaryDimension(
+    prevObsCrossfilter,
+    state,
+    genesetName
+  );
+  dispatch({
+    type: "continuous metadata histogram cancel",
+    continuousNamespace: { isGeneSetSummary: true },
+    selection: genesetName,
+  });
+  return dispatch({
+    type: "geneset: add genes",
+    genesetName,
+    genes,
+    obsCrossfilter,
+    annoMatrix: obsCrossfilter.annoMatrix,
+  });
+};
+
+export const genesetDeleteGenes = (genesetName, geneSymbols) => (
+  dispatch,
+  getState
+) => {
+  const state = getState();
+  const obsCrossfilter = dropGeneset(dispatch, state, genesetName, geneSymbols);
+  return dispatch({
+    type: "geneset: delete genes",
+    genesetName,
+    geneSymbols,
+    obsCrossfilter,
+    annoMatrix: obsCrossfilter.annoMatrix,
+  });
+};
+
+/*
+Private
+*/
+
+function dropGenesetSummaryDimension(obsCrossfilter, state, genesetName) {
+  const { annoMatrix, genesets } = state;
+  const varIndex = annoMatrix.schema.annotations?.var?.index;
+  const gs = genesets?.genesets?.get(genesetName) ?? {};
+  const genes = Array.from(gs.genes.keys());
+  const query = {
+    summarize: {
+      method: "mean",
+      field: "var",
+      column: varIndex,
+      values: genes,
+    },
+  };
+  return obsCrossfilter.dropDimension("X", query);
+}
+
+function dropGeneDimension(obsCrossfilter, state, gene) {
+  const { annoMatrix } = state;
+  const varIndex = annoMatrix.schema.annotations?.var?.index;
+  const query = {
+    where: {
+      field: "var",
+      column: varIndex,
+      value: gene,
+    },
+  };
+  return obsCrossfilter.dropDimension("X", query);
+}
+
+function dropGeneset(dispatch, state, genesetName, geneSymbols) {
+  const { obsCrossfilter: prevObsCrossfilter } = state;
+  const obsCrossfilter = geneSymbols.reduce(
+    (crossfilter, gene) => dropGeneDimension(crossfilter, state, gene),
+    dropGenesetSummaryDimension(prevObsCrossfilter, state, genesetName)
+  );
+  dispatch({
+    type: "continuous metadata histogram cancel",
+    continuousNamespace: { isGeneSetSummary: true },
+    selection: genesetName,
+  });
+  geneSymbols.forEach((g) =>
+    dispatch({
+      type: "continuous metadata histogram cancel",
+      continuousNamespace: { isUserDefined: true },
+      selection: g,
+    })
+  );
+  return obsCrossfilter;
+}