Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Add tooltips to the phylo tree for both NCBI and Sample entries #1532

Merged
merged 5 commits into from Oct 1, 2018
Merged

Add tooltips to the phylo tree for both NCBI and Sample entries #1532

Show file tree
Hide file tree
Changes from 2 commits
Commits
Show all changes
5 commits
Select commit Hold shift + click to select a range
df6cb2f
* Add tooltips to the phylo tree for both NCBI and Sample entries
Sep 28, 2018
aaa2283
Remove access to originating window.
Sep 28, 2018
d82bd33
Merge branch 'master' into tiago/sprint-phylo
tfrcarvalho Oct 1, 2018
c67183a
Add extra fields to tooltip.
Oct 1, 2018
446e941
Merge branch 'tiago/sprint-phylo' of github.com:chanzuckerberg/idseq-…
Oct 1, 2018
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Jump to
Jump to file
Failed to load files.
Diff view
Diff view
47 changes: 47 additions & 0 deletions app/assets/src/components/ui/containers/DataTooltip.jsx
View file
Open in desktop
@@ -0,0 +1,47 @@
import React from "react";
import PropTypes from "prop-types";

const DataTooltip = ({ data, subtitle, title }) => {
// DataTooltip receives:
// - title
// - subtitle
// - an object(section_name: array([label, value], [..]))

const renderSection = (sectionName, dataValues) => {
return (
<div className="data-tooltip__section" key={`section-${sectionName}`}>
<div className="data-tooltip__section-name">{sectionName}</div>
{dataValues.map(keyValuePair => {
return (
<div
className="data-tooltip__value-pair"
key={`value-${sectionName}-${keyValuePair[0]}`}
>
<div className="data-tooltip__label">{keyValuePair[0]}</div>
<div className="data-tooltip__value">{keyValuePair[1]}</div>
</div>
);
})}
</div>
);
};

const renderSections = data => {
return data.map(section => renderSection(section.name, section.data));
};

return (
<div className="data-tooltip">
{title && <div className="data-tooltip__title">{title}</div>}
{subtitle && <div className="data-tooltip__subtitle">{subtitle}</div>}
<div className="data-tooltip__data">{renderSections(data)}</div>
</div>
);
};

DataTooltip.propTypes = {
data: PropTypes.array,
subtitle: PropTypes.string,
title: PropTypes.string
};
export default DataTooltip;
7 changes: 6 additions & 1 deletion app/assets/src/components/views/phylo_tree/PhyloTreeListView.jsx
View file
Open in desktop
Expand Up @@ -28,7 +28,11 @@ class PhyloTreeListView extends React.Component {
}

getDefaultSelectedTreeId(urlParams, phyloTrees = []) {
return urlParams.treeId || (phyloTrees[0] || {}).id;
return (
urlParams.treeId ||
parseInt(window.sessionStorage.getItem("treeId")) ||
Copy link
Contributor

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

did we all agree that window.sessionStorage is OK? is it supported on all the modern browsers

Copy link
Contributor Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Should be fine: https://developer.mozilla.org/en-US/docs/Web/API/Window/sessionStorage. We should do a more through css/js audit for issues in older browsers.

(phyloTrees[0] || {}).id
);
}

resetUrl() {
Expand All @@ -45,6 +49,7 @@ class PhyloTreeListView extends React.Component {
}

handleTreeChange(_, newPhyloTreeId) {
window.sessionStorage.setItem("treeId", newPhyloTreeId.value);
this.setState({
selectedPhyloTreeId: newPhyloTreeId.value
});
Expand Down
120 changes: 99 additions & 21 deletions app/assets/src/components/views/phylo_tree/PhyloTreeVis.jsx
View file
Open in desktop
Expand Up @@ -2,25 +2,38 @@ import React from "react";
import Tree from "../../utils/structures/Tree";
import Dendogram from "../../visualizations/dendrogram/Dendogram";
import PropTypes from "prop-types";
import DataTooltip from "../../ui/containers/DataTooltip";

class PhyloTreeVis extends React.Component {
constructor(props) {
super(props);

this.state = {
newick: props.newick
hoveredNode: null
};

this.treeVis = null;
}
(this.newick = props.newick),
(this.nodeData = props.nodeData),
(this.treeVis = null);

static getDerivedStateFromProps(props, state) {
if (props.newick !== state.newick || props.nodeData !== state.nodeData) {
return {
newick: props.newick,
props: props.nodeData
};
}
this.handleNodeHover = this.handleNodeHover.bind(this);

this.sampleFields = [
{ name: "project_name", label: "Project" },
{ name: "sample_location", label: "Location" },
{ name: "created_at", label: "Upload Date" },
Copy link
Contributor

@cdebourcy cdebourcy Sep 29, 2018 •
edited

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

ideally this would be displayed using <Moment />

Copy link
Contributor Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Good catch. I thought of that when I was adding the field, but forgot to add. Done.

{ name: "sample_date", label: "Collection Date" },
{ name: "sample_tissue", label: "Tissue" },
{ name: "sample_template", label: "Template" },
{ name: "sample_library", label: "Library" },
{ name: "sample_sequencer", label: "Sequencer" },
{ name: "sample_unique_id", label: "Unique ID" },
{ name: "sample_notes", label: "Notes" }
Copy link
Contributor

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

I'm sorry I realized I forgot some:

    t.float "sample_input_pg", limit: 24 # RNA/DNA input (pg)
    t.integer "sample_batch" # Batch
    t.text "sample_diagnosis" # Clinical diagnosis
    t.string "sample_detection" # Detection method

Copy link
Contributor Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Added.

];
this.ncbiFields = [
{ name: "country", label: "Country" },
{ name: "collection_date", label: "Collection Date" }
];
}

componentDidMount() {
Expand All @@ -33,26 +46,91 @@ class PhyloTreeVis extends React.Component {
// Name for the legend when the attribute is missing / other
colorGroupAbsentName: "NCBI References",
legendX: 880,
legendY: 50
legendY: 50,
tooltipContainer: this.tooltipContainer,
onNodeTextClick: this.handleNodeClick,
onNodeHover: this.handleNodeHover
});
this.treeVis.update();
}

componentDidUpdate() {
this.treeVis.setTree(
Tree.fromNewickString(this.props.newick, this.props.nodeData)
);
this.treeVis.update();
if (
this.props.newick != this.newick ||
this.props.nodeData != this.nodeData
) {
this.newick = this.props.newick;
this.nodeData = this.props.nodeData;
this.treeVis.setTree(
Tree.fromNewickString(this.props.newick, this.props.nodeData)
);
this.treeVis.update();
}
}

handleNodeHover(node) {
this.setState({ hoveredNode: node });
}

handleNodeClick(node) {
if (node.data.accession) {
let url = `https://www.ncbi.nlm.nih.gov/nuccore/${node.data.accession}`;
window.open(url, "_blank", "noopener", "noreferrer");
} else if (node.data.id) {
location.href = `/samples/${node.data.id}`;
}
}

getTooltipData() {
let fields = this.state.hoveredNode.data.accession
? this.ncbiFields
: this.sampleFields;

let topSectionName = null;
let topSectionData = null;
if (this.state.hoveredNode.data.project_name) {
topSectionName = "Sample";
topSectionData = [
["Project", this.state.hoveredNode.data.project_name || "-"]
];
} else {
topSectionName = "NCBI Reference";
topSectionData = [
["Accession", this.state.hoveredNode.data.accession || "-"]
];
}
return [
{ name: topSectionName, data: topSectionData },
{
name: "Metadata",
data: fields.map(f => [
f.label,
this.state.hoveredNode.data[f.name] || "-"
])
}
];
}

render() {
return (
<div
className="phylo-tree-vis"
ref={container => {
this.treeContainer = container;
}}
/>
<div className="phylo-tree-vis">
<div
className="phylo-tree-vis__tree-container"
ref={container => {
this.treeContainer = container;
}}
/>
<div
className="phylo-tree-vis__tooltip-container"
ref={tooltip => {
this.tooltipContainer = tooltip;
}}
>
{this.state.hoveredNode && (
<DataTooltip data={this.getTooltipData()} />
)}
</div>
</div>
);
}
}
Expand Down
88 changes: 47 additions & 41 deletions app/assets/src/components/visualizations/dendrogram/Dendogram.js
View file
Open in desktop
Expand Up @@ -14,7 +14,18 @@ export default class Dendogram {

this.options = Object.assign(
{
curvedEdges: false
curvedEdges: false,
defaultColor: "#cccccc",
colormapName: "viridis",
colorGroupAttribute: null,
colorGroupLegendTitle: null,
colorGroupAbsentName: null,
legendX: 880,
legendY: 50,
onNodeTextClick: null,
onNodeClick: null,
onNodeHover: null,
tooltipContainer: null
},
options || {}
);
Expand All @@ -28,7 +39,7 @@ export default class Dendogram {
// margin top
this.margins = {
// includes legend
top: 60,
top: 80,
// includes second half of nodes
bottom: 20,
// includes root label on the left of the node
Expand Down Expand Up @@ -70,10 +81,7 @@ export default class Dendogram {
`translate(${this.margins.left}, ${this.margins.top})`
);

this.tooltipDiv = select("body")
.append("div")
.attr("class", "dendogram__tooltip")
.style("opacity", 0);
this.tooltipContainer = select(this.options.tooltipContainer);
}

adjustHeight(treeHeight) {
Expand Down Expand Up @@ -541,48 +549,42 @@ export default class Dendogram {
})
.attr("transform", function(node) {
return `translate(${node.y},${node.x})`;
});

if (!this.tooltipContainer.empty()) {
nodeEnter
.on("mouseenter", node => {
if (!node.children) {
this.options.onNodeHover && this.options.onNodeHover(node);
this.tooltipContainer.classed("visible", true);
}
})
.on("mousemove", node => {
if (!node.children) {
this.tooltipContainer
.style("left", currentEvent.pageX + 20 + "px")
.style("top", currentEvent.pageY + 20 + "px");
}
})
.on("mouseleave", () => {
if (!node.children) {
this.tooltipContainer.classed("visible", false);
}
});
}

nodeEnter
.append("circle")
.attr("r", function(node) {
return node.children ? 3 : 5;
})
.on("click", node => {
this.clickHandler(
() => this.markAsHighlight(node),
() => this.rerootOriginalTree(node)
);
})
.on("mouseover", node => {
if (!node.children) {
let md = node.data.name.split("__");
md.shift();

if (md.length > 0) {
this.tooltipDiv.html(md.join(" / "));

this.tooltipDiv
.transition()
.duration(200)
.style("opacity", 0.9);
}
}
})
.on("mousemove", node => {
if (!node.children) {
this.tooltipDiv
.style("left", currentEvent.pageX + 20 + "px")
.style("top", currentEvent.pageY + 20 + "px");
}
})
.on("mouseout", () => {
if (!node.children) {
this.tooltipDiv
.transition()
.duration(500)
.style("opacity", 0);
}
});

nodeEnter.append("circle").attr("r", function(node) {
return node.children ? 3 : 5;
});

nodeEnter
.append("text")
.attr("dy", function(d) {
Expand All @@ -593,7 +595,11 @@ export default class Dendogram {
})
.text(function(d) {
return d.children ? "" : d.data.name.split("__")[0];
});
})
.on(
"click",
d => this.options.onNodeTextClick && this.options.onNodeTextClick(d)
);

if (this.options.colorGroupAttribute && !this.skipColoring) {
// Apply colors to the nodes from data.colorIndex
Expand Down
1 change: 1 addition & 0 deletions app/assets/src/loader.scss
View file
Open in desktop
Expand Up @@ -40,6 +40,7 @@
@import "styles/ui/labels/pathogen_label";

// ui/containers
@import "styles/ui/containers/data_tooltip";
@import "styles/ui/containers/modal";
@import "styles/ui/containers/wizard";

Expand Down