Plot Dashboard

Core Feature

This feature is available in all Portrai Explorer deployments.

The Plot Dashboard is the shared workspace for every chart in Portrai Explorer. Instead of one chart at a time, you build a grid of independent plot panels — a scatter of two genes next to a violin of expression across clusters next to a dot plot of marker genes — and arrange them side by side to read your data from several angles at once.

It plays the role of a notebook full of matplotlib/seaborn figures or a panel of ggplot2 charts, except every panel stays live and linked to the same dataset. The plots themselves mirror their single-cell equivalents (Seurat's VlnPlot/DotPlot, scanpy.pl.*), while the dashboard adds the layout, naming, and persistence that hold a multi-figure analysis together. This page covers the workspace model that all six plot types share; see the per-type docs for the controls specific to each.

Opening the Plot Extension

1. Click the Plot icon in the Activity Bar (left side)
2. The Sidebar opens with the Plots panel (the plot list) and the Settings panel (the active plot's inspector)
3. The Workspace shows the plot grid

When a project has no plots yet, the workspace shows an empty state reading "No plots yet" with a prompt to "Click '+ New Plot' in the sidebar to add one."

The Plot Catalog

Adding a plot starts from the + New Plot button at the top of the Plots sidebar panel. It opens a catalog of the six plot types:

Plot Type	What it shows	Doc
Scatter Plot	Relationship between two variables — embeddings or gene vs gene	Scatter Plot
Bar Plot	Aggregate a value (mean/sum/…) per category	Bar Plot
Stacked Bar Plot	Composition of one category within another (count or %)	Stacked Bar Plot
Violin Plot	Compare value distributions across groups	Violin Plot
Dot Plot	Gene × group: dot size = % expressing, color = mean	Dot Plot
Box Plot	Distribution summary per group (median, IQR, outliers)	Box Plot

Adding a Plot

Selecting a type from the catalog creates the plot immediately and makes it the active plot — there is no separate "Create" step. The new panel:

• Is titled with the type name plus a running ordinal (for example, the second violin you add is named "Violin Plot 2").
• Is auto-placed at the bottom of the grid, and the workspace scrolls to bring it into view.
• Opens its Settings inspector in the sidebar so you can configure it right away.

TIP

Because plots are created already-live, the way to discard one is to delete it — there is no cancel button. A freshly added plot with no axes or variables selected simply renders empty until you configure it.

Plot Panel Anatomy

Each plot lives in its own panel. The panel's titlebar (the bar across the top) is where you manage that plot:

Control	Description
Title	The plot's name. Double-click it to rename inline.
⋯ menu	Per-plot actions: Rename, Duplicate, Delete.
Toolbar slot	The active renderer's Export and Layer Settings controls appear here.
✕ close	Deletes the plot.

INFO

The Export and Layer Settings buttons live in each panel's own titlebar, beside the ⋯ menu and ✕ button — not in a separate floating toolbar. Each plot type's renderer supplies its own controls into that slot, so the exact buttons depend on the plot type. See Layer Settings and Image Export.

Clicking anywhere on a panel makes it the active plot.

Rename

You can rename a plot three ways, all editing the same title:

• Double-click the title in the panel titlebar (or the name in the sidebar list).
• Open the panel's ⋯ menu and choose Rename.
• Open the sidebar list row's ⋯ menu and choose Rename.

Press Enter or click away to commit; press Escape to cancel. In the sidebar list, an empty name is ignored and the previous name kept.

Duplicate

Duplicate (from either ⋯ menu, or the keyboard shortcut below) creates a full copy of the plot — same type and configuration — with "(copy)" appended to its title. The copy is placed at the bottom of the grid.

Delete

Remove a plot with the ✕ button, the Delete action in either ⋯ menu, or the keyboard shortcut. Deleting the active plot clears the Settings inspector.

Repositioning Labels

A plot's axis titles and its legend (or colorbar / size legend, where the plot type has one) can be dragged to a better spot — drag the label itself to move it. Positions are stored per plot as a ratio of the panel size, so they stay put when you resize the panel and persist with the rest of the dashboard.

Once you've moved at least one label, a Reset label positions button appears in that panel's titlebar toolbar (beside Export and Layer Settings); it returns every label to its default placement. The button stays hidden until there's something to reset.

Keyboard Shortcuts

When a plot is active (and you are not typing in a field), these shortcuts apply:

Shortcut	Action
Delete / Backspace	Delete the active plot
Ctrl/Cmd + D	Duplicate the active plot

TIP

Shortcuts are ignored while you are typing in an input, text area, or select — so editing values in the Settings inspector never accidentally deletes a plot.

Arranging the Grid

Panels live in a responsive grid you can rearrange freely:

• Reposition — drag a panel by its titlebar to move it. Other panels reflow (the grid compacts upward to fill gaps).
• Resize — drag a panel's bottom or side edges, or either bottom corner (south, west, east, and the south-west/south-east corners). The top edge is intentionally not resizable: the grid keeps panels pulled to the top, so resizing upward would fight compaction. Panels have a minimum size so a plot always has room to render. Dragging the handle near the workspace's bottom edge auto-scrolls the workspace down, so a panel can grow past the current viewport.
• Reorder from the sidebar — dragging a row in the sidebar plot list rearranges the panels to match that order.
• Auto-arrange — the Auto-arrange button in the workspace top bar (next to Define Subset) repacks every panel into a tidy masonry layout, dropping each plot into the currently-shortest column to minimize vertical gaps. It is disabled until there are at least two plots.

The grid adapts its column count to the available width, so panel positions reflow on narrower screens.

The Sidebar Plot List

The Plots panel in the sidebar lists every plot in the current project. Each row shows the plot's type icon and its title.

• Ordering mirrors the grid — rows are listed in the grid's visual reading order (top to bottom, then left to right), and the list and grid stay in sync both ways: rearranging panels in the workspace re-sorts the list, and reordering rows rearranges the panels.
• Drag to reorder — drag a row up or down to change the plot order; the whole row is the drag handle. The panels on the canvas rearrange to match the new order while keeping the grid's column layout. On a touch screen, press and hold a row briefly before dragging — a quick swipe scrolls the list instead.
• Click to scroll — clicking a row makes that plot active and scrolls its panel into view, which is handy when the grid is taller than the screen.
• Per-row ⋯ menu — the same Rename, Duplicate, and Delete actions as the panel titlebar.

The Active Plot and Its Settings

Exactly one plot is active at a time. The active plot is highlighted both in the grid and in the sidebar list, and its configuration is shown live in the sidebar Settings panel (the inspector).

• A plot becomes active when you create it, click its panel, or click its row in the sidebar list.
• The Settings inspector shows the controls for the active plot's type — the same selectors documented in each per-type page. Edits apply immediately; there is no apply/save step.
• When no plot is active, the inspector shows a hint: "Select a plot to view its settings, or click '+ New Plot' to create one."

For Scatter plots colored by a feature or signature, an extra Details panel appears in the sidebar with statistics for the current color-by selection (see Scatter Plot).

Define Subset Is Workspace-Global

A single Define Subset control sits at the top of the Plot workspace, above the grid (the Auto-arrange button sits beside it on the right). It is shared by every plot — there is one subset definition for the workspace, not one per panel. Changing the subset re-filters the points feeding all plots at once, keeping panels comparable.

See Subset and Lasso Selection for how subset conditions are built (including lasso selections drawn directly on a scatter plot).

Per-Project Persistence

The dashboard is saved per project and survives page reloads:

• The full set of plots — their types, titles, configurations, and grid layout — is stored under that project's own bucket.
• Which plot is active is also remembered per project.

Switching projects loads that project's own plots; a project's dashboard never leaks into another. Opening a project restores exactly the layout you left, including the previously active plot.

Use Cases

Multi-Angle Marker Review

1. Add a Dot Plot of candidate marker genes across clusters.
2. Add a Violin Plot of one promising marker to inspect its full distribution.
3. Add a Scatter Plot of two co-markers to check co-expression.
4. Arrange the three panels side by side and read them together.

Composition vs. Abundance

1. Add a Stacked Bar Plot of cell-type composition per sample.
2. Add a Bar Plot of a QC metric (mean counts) per sample beside it.
3. Define a workspace subset to focus on a region of interest — both update together.

Iterating on a Figure

1. Configure a plot, then Duplicate it (Ctrl/Cmd + D).
2. Tweak the copy's settings (different gene, scale, or grouping).
3. Compare the original and the variant side by side, then delete whichever you don't keep.

Troubleshooting

Workspace Shows "No plots yet"

The current project has no plots. Click + New Plot in the sidebar to add one.

A Plot Panel Is Empty

A plot renders empty until it is configured. Open it (click the panel) and set its required selectors in the Settings inspector — see the relevant per-type doc. Also confirm the workspace subset isn't excluding all points.

Settings Panel Shows a Hint Instead of Controls

No plot is active. Click a panel in the grid or a row in the sidebar list to activate one.

My Plots Disappeared After Switching Projects

Plots are stored per project. Each project keeps its own dashboard — switch back to the original project to see its plots again.

Can't Drag a Panel

Drag from the panel titlebar, not the plot body. Dragging inside the plot area is reserved for plot interactions (pan, lasso, hover).

Related Topics

• Scatter Plot - Two-variable relationships and lasso selection
• Violin Plot - Distribution comparison across groups
• Bar Plot - Aggregate a value per category
• Stacked Bar Plot - Composition within a category
• Dot Plot - Gene × group expression summary
• Box Plot - Per-group distribution summary
• Layer Settings - Per-plot appearance controls
• Color Mapping - Configure plot color scales
• Subset - Workspace-global point filtering
• Image Export - Export a plot as an image