Charts

Charts are graphical representations of the measurement data on the FOV. User can choose from several types of charts to plot the measurement data.

The chart toolbar allows the user to invoke various commands that are common to most charts. Some commands are disabled depending on which chart is selected.

Select chart
Select the chart you want to display by using this dropdown.

Selection cursor
Mode that makes it so that clicking or dragging on a chart selects features.

Zoom
Mode that makes it so that selecting a region on the chart zooms into that region.

Reset chart axes
Resets the axes range of the chart to their default values.

Toggle legend
Shows or hides the chart legend.

Export chart to diagram file
Saves the visual of the chart to a file.

Copy chart to clipboard
Copies an image of the chart to a clipboard.

Copy chart data to clipboard
Copies the chart data to the clipboard. The format of the data depends on the chart.

Add chart to summary report
Copies the chart data to the clipboard. The format of the data depends on the chart.

On this page:

General usage

Plot measurements

You can specify the measurements to plot in the Charts panel by changing the axis measurements. To select an axis measurement, use the selection box(es) in the upper left of the chart or use the arrows underneath, left or right of the axis label. The axis title will change to the selected measurement and the chart data will be refreshed to show the new measurements.

Change axis scale

To change the scale on any axis, click on the minimum or maximum value displayed (indicated by a small pencil icon) and that value will appear in an editable window. Type in the value you want for that end of the axis and hit Enter. Repeat this for any endpoint value you wish to change.

Additional display options

In general, options for a given chart can be accessed by right-clicking on the chart itself to display the context menu. The context menu is specific to each chart. For details regarding chart options, please refer to the documentation related to the chart of interest.

Legend

The charts: Histogram, Scatter plot and Binned Scatter plot have a collapse-/expandable legend indicating which object sets/subsets are displayed within the chart. To show/hide object sets/subsets de/select them from the legend.


Example plot (Scatter plot), including measurement-selection boxes (upper left) and legend (upper right)

Types of charts

Aivia has thirteen types of charts:

Chart Type	Icon	Description
Histogram		Presents the data for one object set as a binned distribution. Each bar in the Histogram represents the aggregate total number of objects whose measurement values fall within a given range.
Scatter plot		Allows the user to graph one measurement against another measurement. Each object is represented as a single dot in the chart.
Binned Scatter plot		Allows the user to graph one measurement against another measurement. The display area is binned, objects within those bins are counted and their counts visualized accordingly.
Trace plot		The default charting option for all data with a time component. It displays a single measurement of selected objects over time. The measurement value is plotted on the y-axis and time on the x-axis. Trace Plot can display data from a single object, whole FOV, or multiple objects simultaneously.
Directional plot		Takes selected tracks from the data set and places the start point at the origin to show the migration patterns of selected tracks.
Lineage plot		Displays a single-track object at any given time to show when the track splits into two daughter tracks.
Flow plot		An enhanced lineage representation, the width and color of this chart are plotted against time to show the evolution of selected track objects and their respective lineages.
Kymograph		Depicts of time-related data and creates a new image with defined physical coordinates on the x-axis and time on the y-axis.
Pearson heatmap		Calculates the Pearson correlation coefficient between pairs of all measurements and presents them color-coded in a heatmap.
Violin plot		Displays the probability density function for one measurement, adds a swarm or box and whisker plot as an overlay and displays the significance of the mean values according to Welch's t-test.
Summary View		Displays summary measurements (mean (+/- sd or sem), min, max, total) for object set/subsets as a bar graph.
Dendrogram		Is a tree-like diagram that displays the hierarchical structure of data.
Dimensionality Reduction		Displays the relationships between data points in a reduced dimensional space.