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Pivot Tables

Pivot tables are grids of 1D (histogram) or 2D (biaxial) flow plots. After selecting FCS file annotations, population names or channel names to use for the rows and columns of the grid, files are automatically selected to populate the figure.

A single FCS file can be displayed per position in the grid. If zero files match, or if more than one file matches, then the position will appear blank. Hover over the blank position for an explanation of why it is blank. If multiple files match, filter annotations can be used to reduce the number of matching files (see filter annotations described in the pivoting model).

Pivot tables can be nested to contain more than two dimensions (i.e. more than "rows" and "columns"), up to 10 levels, by clicking the add table button. For large pivot tables, also consider a batched illustration to create a multi-page view.

Examples

These examples show small pivot tables for simplicity. However, pivot tables may contain hundreds or thousands of selections in each dimension.

Basic pivot table

basic pivot table example

Howto

  1. Insert a pivot table using the pivot table icon button in the toolbar.
  2. Set up the pivot table dimensions as described in the pivoting model. In the example above, the settings are as follows:
    • Columns Populations: CD4- T cells, CD4+ T cells, CD20+, CD33+ Monos/DCs
    • Rows Condition: IL2/GM-CSF, IL10, Unstim
  3. Select the X and Y channels and other settings in the sidebar and toolbar as desired.

Histogram overlays

histogram overlay example

Howto

  1. Insert a pivot table using the pivot table icon button in the toolbar.
  2. In the top toolbar, change the plot type to histogram.
  3. Set up the pivot table dimensions as described in the pivoting model. In the example above, the settings are as follows:
    • Columns Populations: CD4- T cells, CD4+ T cells, CD20+, CD33+ Monos/DCs
    • Rows Condition: IL2/GM-CSF, IL10, LPS, PMA, Unstim
    • Table 1 X Channels: pStat3, pStat5
  4. Check the Overlay box for the dimension to overlaid. In the example above, the rows (condition) dimension is overlaid. Adjust the pitch as desired.
  5. As desired, adjust the histogram fill opacity near the bottom of the sidebar and the plot smoothing in the top toolbar.

N x N (channel by channel) plots

N by N example

Howto

  1. Insert a pivot table using the pivot table icon button in the toolbar.
  2. In the right sidebar, set the Columns dimension name to X Channels. In the values selector, pick which channels to display.
  3. Set the Rows dimension name to Y Channels. In the values selector, select Same as X Channels at the top.
  4. Set general parameters such as filter annotations, the FCS file, population and gate labels in the sidebar.
  5. For a simpler view like the one shown above, go to the Axes and Legend section and turn off tick marks and axis labels.
  6. Change label font sizes or move column labels to the bottom of the table by choosing options in the Pivot Table section.

Tip

To view the N x N illustration for each file or annotation combination, turn on batched illustration mode.

Common Settings

Adjusting the order of values

When you select annotations, populations and channels, they will be automatically sorted. However, you can override the default sorting by following the instructions in annotation, population and channel sorting.

Change gate appearance

By default any gates in a pivot table plot will be shown, along with the percent of events contained within the parent gate.

The Gates section allows you to:

  • Show/hide gates in the pivot table
  • Change label size of gates
  • Change a gate label to the gate name or a statistic about the gated population.

Tip

To adjust the gate shown in a plot, right-click on the plot and click View in gating.

Dimension spacing and label size

In the sidebar under Pivot Table, a font size and spacing section allows adjusting the following settings for each dimension:

  • The label font size
  • The label visibility (show/hide)
  • Spacing between dimension values

To keep labels visible as you scroll:

Howto

  1. Click on the View menu.
  2. Select Sticky Labels.

Collapsing empty rows and columns

In some experiments, a pivot table may be sparse, meaning that not every combination of every annotation value exists. For example, in a clinical trial with annotations for "donor ID" and "timepoint," not every donor might have been sampled at every timepoint. In experiments with at least three annotation columns, this sparsity can result in entire rows and/or columns that are blank.

To collapse these blank rows and columns, toggle on the collapse empty rows and columns option in the Pivot Table section of the sidebar.

Plot styling

The Axes and Legend section controls allow turning on and off tick marks, tick labels and axis labels.