Illustrations let you visualize your data and create figures for slides and publications.
Illustrations can be either used in single-page mode, or in batched layout mode. Batched illustrations allow you to create a template page, and then render that page for each value in a set of variables. For example, you could use flow plots, text boxes and arrows to create a gating hierarchy, and then render that gating hierarchy for all of your FCS files.
To create a new, empty illustration:
- In the left sidebar, click on New Illustration. A new illustration will opened with the name highlighted.
- Type in the name of the illustration.
To duplicate an existing illustration:
- Illustrations, click on the File menu, and then Duplicate Illustration.
- the Summary of an experiment, right-click on the name of the illustration, and click on Duplicate.
A variety of visualization types are available:
Flow Plots Individual 1D and 2D flow plots (histograms and biaxials). Ideal for creating gating hierarchies when used in conjunction with arrows and text boxes.
Pivot Tables: Grids of flow plots, optionally overlaid.
Heatmaps: A grid of statistics.
Bar and Line Charts: Summary figures that display channel statistics or population frequencies.
Box Plots: Display information about the distribution of datapoints, such as the median and interquartile range. Ideal for looking at experiments with many replicate conditions.
Dose Response Curves: Calculate the relationship between the dosage of a drug and a readout.
Basic Objects, including text boxes, images, lines and arrows.
Illustration functionality is accessible from the menus, toolbars and sidebar. Menus and toolbars allow you to place graphs and change illustration settings, while sidebars control the data and appearance of individual elements.
When selected, the text box adds additional toolbar options:
Customizing Data Visualization¶
The pivoting model¶
Pivot tables, bar charts, line charts, heatmaps and box plots all use a pivoting model to organize the data that they display. After selecting FCS file annotations to display along the X and Y dimensions (rows and columns, or axis labels and data series), files are automatically selected to populate the figure. You can also select populations or channels as X/Y dimensions, or explicitly select FCS files by filename.
Filter annotations may also be selected to limit the files displayed. For example, if you select “Plate Row” for your “rows” dimension and “Plate Column” for your “column” dimension, but have several 96-well plates in your experiment, you can use “Plate: plate 1” as a filter annotation to show data from just “plate 1.”
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.
Downloading an illustration as a PDF¶
- From your illustration, click the File menu, then select Print to PDF.
Downloading parts of an illustration as SVG, PNG or PDF¶
Some types of components can be downloaded as SVG, PNG and/or PDF files.
- In your illustration, select one component.
- In the right-hand sidebar, click Download PNG/PDF/SVG.
Copying and pasting to other applications¶
You can copy illustrations or parts of illustrations to other programs, such as Microsoft Office and Apple iWork applications. All selected components will be rendered into a single image when they are copied.
- Select one or more components in an illustration.
- Use the keyboard shortcut to copy the selection.
- In the destination application, use the keyboard shortcut to paste.
Changing page size for print or presentation¶
By default, each illustration has a generous area to position large numbers and sizes of graphs. However, you can change the size to common printing and presentation sizes and orientations. The available sizes are:
- Extra large (200 x 200 in)
- Letter portrait (8 ½ x 11 in)
- Letter landscape (11 x 8 ½ in)
- A4 portrait (210 x 297 mm)
- A4 landscape (297 x 210 mm)
- 4:3 standard slide (10 x 7.5 in)
- 16:9 widescreen slide (10 x 5 ⅝ in)
To change the size or orientation of an illustration:
- In the illustration view, click on File.
- Mouse over Page Size ->.
- Click on your desired size.