experimental re-embedding (#1186)

* first cut at re-embedding route and back-end support * update and expand config route tests * add scanpy_umap * add reembedding to config route parameters * front-end support for reembedding fetch and UI * remove unused imports * add loading state * save reembedding in reducer state * improve withColsFrom * transmit reembed schema to client; pick unique embedding names * display embeddings * format * lint * spaces, tab size 2 * lint * test hack for smoke-test race * back out hack sleep * add check for backed mode * add unit test for reembedding * lint * hide re-embedding CLI param from help
2026-09-30 07:38:12 +08:00 · 2020-03-09 16:53:30 -07:00
parent b3e9719602
commit 144b19c449
25 changed files with 928 additions and 159 deletions
@@ -0,0 +1,122 @@
+import React from "react";
+import {
+  AnchorButton,
+  ButtonGroup,
+  Popover,
+  Button,
+  Radio,
+  RadioGroup,
+  Tooltip,
+  Position
+} from "@blueprintjs/core";
+import { connect } from "react-redux";
+import * as globals from "../../globals";
+import { World } from "../../util/stateManager";
+import actions from "../../actions";
+
+@connect(state => ({
+  universe: state.universe,
+  world: state.world,
+  layoutChoice: state.layoutChoice,
+  reembedController: state.reembedController,
+  enableReembedding: state.config?.parameters?.["enable-reembedding"] ?? false
+}))
+class Embedding extends React.PureComponent {
+  handleLayoutChoiceChange = e => {
+    const { dispatch } = this.props;
+    dispatch({
+      type: "set layout choice",
+      layoutChoice: e.currentTarget.value
+    });
+  };
+
+  renderReembedding() {
+    const {
+      enableReembedding,
+      world,
+      universe,
+      dispatch,
+      reembedController
+    } = this.props;
+
+    if (!enableReembedding) return null;
+
+    const loading = !!reembedController?.pendingFetch;
+    const disabled = World.worldEqUniverse(world, universe);
+    const tipContent = disabled
+      ? "Subset cells first, then click to recompute UMAP embedding."
+      : "Click to recompute UMAP embedding on the current cell subset.";
+
+    return (
+      <Tooltip
+        content={tipContent}
+        position="bottom"
+        hoverOpenDelay={globals.tooltipHoverOpenDelay}
+      >
+        <AnchorButton
+          icon="new-object"
+          style={{ marginRight: 10 }}
+          disabled={disabled}
+          onClick={() => dispatch(actions.requestReembed())}
+          loading={loading}
+        />
+      </Tooltip>
+    );
+  }
+
+  render() {
+    const { layoutChoice } = this.props;
+
+    return (
+      <ButtonGroup
+        style={{
+          marginRight: 10
+        }}
+      >
+        <Popover
+          target={
+            <Tooltip
+              content="Select embedding for visualization"
+              position="bottom"
+              hoverOpenDelay={globals.tooltipHoverOpenDelay}
+            >
+              <Button
+                type="button"
+                data-testid="layout-choice"
+                icon="heatmap"
+                style={{
+                  cursor: "pointer"
+                }}
+              />
+            </Tooltip>
+          }
+          position={Position.BOTTOM_RIGHT}
+          content={
+            <div
+              style={{
+                display: "flex",
+                justifyContent: "flex-start",
+                alignItems: "flex-start",
+                flexDirection: "column",
+                padding: 10
+              }}
+            >
+              <RadioGroup
+                label="Embedding Choice"
+                onChange={this.handleLayoutChoiceChange}
+                selectedValue={layoutChoice.current}
+              >
+                {layoutChoice.available.map(name => (
+                  <Radio label={name} value={name} key={name} />
+                ))}
+              </RadioGroup>
+            </div>
+          }
+        />
+        {this.renderReembedding()}
+      </ButtonGroup>
+    );
+  }
+}
+
+export default Embedding;