Skip to content

Reporting

Introduction

Phaedra can generate reports from your data, allowing you to obtain a high-level overview of the data in a clean and presentation-oriented format.

Reports are generated in the PDF file format, and can work in two ways:

  • Ad-hoc reports are generated from scratch, by adding views to a blank page and arranging the layout manually. These are "one-off" reports.
  • Template reports are generated from predefined templates which already contain layout and formatting information. These reports are reusable across plates and experiments.

Any user can generate a report, provided they have read access to the data being added to the report.

Installation

To install the Reporting addon, select Help > Install New Software. In the site list, select Phaedra Updates. Check the Reporting item in the addon list, and click Next.

Ad-hoc Reports

Ad-hoc reports do not follow a predefined template, but are created from scratch. You start with a blank report and fill it up by adding any number of Phaedra views onto the report.

Note: ad-hoc reports are not reusable. When you add a view to the report, the contents of that view in the report are exactly what they were the moment the view was added: the plate(s) being shown, the wells, the selected feature, etc. An ad-hoc report represents a snapshot of data in Phaedra.

To start creating an ad-hoc report, select the menu Window > Show View > Other... > Reporting > Report Designer.

reporting4.png

In the Report Designer view, select the protocol you would like to create a report for, then click the New Report button.

reporting5.png

In the dialog that appears, enter a unique name for the new report, and click Ok. This will create a new, blank report, ready to be filled out by adding views into it.

To add a view, open it like you would open a view normally. For example, to open a Quick Heatmap view, right-click on a plate and select Show Quick Heatmap.

reporting6.png

Configure the view exactly like how you want it to appear in the report. When you are ready, click on the Reporting button and select Save view.

reporting8.png

Enter a unique name for the view and click Ok. By saving the view, you have created a 'snapshot' of the view's configuration. You can add this to the report by clicking on the Reporting button again, and selecting Add to report.

reporting7.png

In the dialog that appears, select the report you just created, and click Ok.

The view will be added as a new page to the blank report. You will be asked to enter a title for the page, as well as an optional description which will be printed below the view in the report.

reporting9.png

If you look at the Report Designer view again, note that the view has been added to the list of views for the new report.

reporting10.png

You can continue adding views to the report in this fashion. Note that the report design is saved automatically every time you add, remove or modify a view. When the report design is finished, you can generate the report by clicking on the Print Report button.

reporting11.png

The report will be generated according to your design. When it is ready, the PDF will open in a separate view.

reporting12.png

To save the report, click on the Save button in the top left of the PDF view.

Template Reports

Template reports are based on a template, and can be generated by selecting an experiment and running the Report Wizard on it. To do this, right-click on an experiment and select Create Report.

reporting.png

The Report Wizard will open, asking you to select one of the available templates.

reporting2.png

Click Next to proceed.

reporting3.png

In this screen, you can select the features which should be included in the report.

Many report templates contain feature-specific pages, such as charts. If you select multiple features, those pages will be repeated for each selected feature. Report templates that do not contain feature-specific pages, will not show this screen.

Click Finish to create the report. When the report is ready, it will appear in a PDF Viewer:

reporting13.png

Use the Save button to save the PDF to your computer, or the Print button to print it out.

Creating a Report Template

To create a new Report Template, the same steps must be followed as during the creation of an ad-hoc report. However, the report and the views must be configured in a different manner. The configuration is explained in this topic.

Start by creating a new report in the Report Designer view, which can be opened via the menu Window > Show View > Other... > Reporting > Report Designer.

reporting4.png

When the Designer appears, switch it into the Template mode by toggling the Template mode button:

reporting-template-1.png

Then, select the protocol you would like to create a report template for, and click the New Report button.

reporting5.png

In the dialog that appears, enter a unique name for the new report. Make sure the following Template Settings are set correctly:

  • Template: this setting must be checked to turn the report into a report template.
  • Global: this setting can be checked to mark the template as "protocol-independent". Global templates can be used on any experiment in any protocol. Note that this means the template cannot contain any views that are feature-specific, as features are themselves protocol-specific.
  • Add Data Summary Page: check this setting to automatically include a Data Summary page at the beginning of the report. This page will list the plates that are included in the report, the number of wells included, how many samples, controls and empties, how many rejected wells, etc.
  • Add Feature Statistics Page: check this setting to automatically include a Feature Statistics page at the beginning of the report. This page will list the features included in the report, along with a table of statistics (mean, median, quartiles, etc) for that feature, for each well type.
  • Grouped By Feature: check this setting to group the report pages by feature. For example, if a report contains two views, Quick Heatmap (QHM) and Well Scatterplot, and two features, then the pages will be ordered as: QHM - Feature 1, QHM - Feature 2, Scatterplot - Feature 1, Scatterplot - Feature 2. By using this setting, the pages will be ordered instead as: QHM - Feature 1, Scatterplot - Feature 1, QHM - Feature 2, Scatterplot - Feature 2.
  • Default Features: when you use a report template on an experiment, you will be asked to select the features to include in the report. With this setting, you can determine which features will be selected by default. Note that a user can always choose a different set of features, this setting merely determines the default selection.

When all settings have been made, click Ok. This will create a new, blank report template, ready to be filled out by adding views into it.

Addings Views to a Report Template

The process of addings views onto a Report Template works very similar to how views are added onto an ad-hoc report. However, some additional configuration must be made to the saved view, before it can work on a report template.

To add a view, open it like you would open a view normally. For example, to open a Quick Heatmap view, right-click on a plate and select Show Quick Heatmap.

reporting6.png

Configure the view exactly like how you want it to appear in the report. When you are ready, click on the Reporting button and select Save view.

reporting8.png

Enter a unique name for the view, make sure the check the "Template" setting and click Ok.

reporting-template-2.png

By saving the view, you have created a 'snapshot' of the view's configuration. You can add this to the report by clicking on the Reporting button again, and selecting Add to report.

reporting7.png

In the dialog that appears, select the report tempalate you just created, and click Ok. Note that report templates have the suffix "T" appended to their names.

The view will be added as a new page to the blank report. You will be asked to enter a title for the page, as well as an optional description which will be printed below the view in the report.

reporting-template-3.png

Make sure to set the Template Settings properly:

  • All features: This setting is deprecated and has no functionality. It will be removed in a future update.
  • Default Input: This setting determines how a view is repeated when the report template is used on an experiment.

The Default Input setting can have one of four values:

  • If the value is set to Single, then the page is repeated for each single entity the view works on.
  • If the value is set to Parent, then the page is repeated once for each parent of the entity the view works on.
  • If the value is set to Parent of Parent, then the page is repeated once for each grandparent of the entity the view works on.
  • If the value is set to All, then the page is not repeated and will try to display all entities in one page.

To illustrate this, consider a Quick Heatmap (QHM) view. This view works on plates, but can only display one plate at a time. Therefore, a setting of Single would repeat the QHM for each plate in the experiment. By contrast, a setting of Parent would repeat the QHM page for each parent of the plate, which is the experiment. But since a QHM can only display a single plate, the report would only show the first plate of each experiment, which is probably not the desired effect.

Another example: the Plate Trend Chart view works on plates, but can display multiple plates at once. In fact, this view is only useful if it shows multiple plates, so in this case it makes sense to set the Default Input to Parent, which will result in one chart per experiment.

As a third example, consider the Well 2D Scatterplot view. This view works on wells, and can display many wells at once. Using a setting of Single, resulting in one plot per well, containing a single data point each, makes little sense. Using a setting of Parent, would result in one plot per parent of well, i.e. one plot per plate. Using a setting of All, would result in a single plot containing all the wells of all the plates in the report.