This topic is under construction for the 17.3 release of LabKey Server. For current documentation of this feature, click here.
Create a Scatter Plot
Change Chart Layout
The Chart Layout
button offers the ability to change the look and feel of your chart.
There are four tabs:
- Provide a title to display on the plot. The default is the name of the source data grid.
- Provide a subtitle to display under the title.
- Specify a width and height.
- Choose whether to jitter points.
- Control the point size and opacity, as well as choose the default color palette. Options: Light (default), Dark, and Alternate. The array of colors is shown under the selection.
- Group By Density: Select either "Always" or "When number of data points exceeds 10,000."
- Grouped Data Shape: Choose either hexagons or squares.
- Density Color Palette: Options are blue & white, heat (yellow/orange/red), or select a single color from the dropdown to show in graded levels. These palettes override the default color palette and other point options in the left column.
- Change the display labels for the axis (notice this does not change which column provides the data).
- Choose log or linear scale for the Y-axis, and specify a range if desired.
- Developer: Only available to users that are members of the "Site Developers" permission group.
Example: Heat Map
Displaying a scatter plot as a heatmap is done by changing the layout of a chart. Very large datasets are easier to interpret as heatmaps, grouped by density (also known as point binning).
- Click Chart Layout and change Group By Density to "Always".
- Select Heat as the Density Color Palette and leave the default Hexagon shape selected
- Click Apply to update the chart with the selected changes.
- Notice that when binning is active, a warning message will appear reading: "The number of individual points exceeds XX. The data is now grouped by density which overrides some layout options." XX will be either 10,000 or 1, if you selected "Always" as we did. Click Dismiss to remove that message from the plot display.
Save and Export Plots
- When your plot is finished, click Save.
- Name the plot, enter a description (optional), and choose whether to make it viewable by others. You will also see the default thumbnail which has been auto-generated, and can choose whether to use it. As with other charts, you can later attach a custom thumbnail if desired.
Once you have saved a scatter plot, it will appear in the Data Browser
and on the
(charts) menu for the source dataset. You can manage metadata about it as described in Manage Data Views
Hover over the chart to reveal export option buttons in the upper right corner:
Export your completed chart by clicking an option:
- PNG: create a PNG image.
- PDF: generate a PDF file.