Results

Results

Overview

In PlateEditor, Results refer to files in which the numerical data to analyze are stored. These are typically the files obtained from plate readers, or any device able to work with multi-well plates.
Attaching, parsing and mapping the result files can be done as explained on the [Data Import] page. Multiple file types are accepted in PlateEditor, including tab-separated or comma-separated (csv) files, but also excel files, both from the old (xls) and new (xlsx) generation. Although other formats are not supported, the relevant contents can be copy/pasted using the manual input function of the import form.
The files should be structured with columns and rows, and must include a column indicating the well name. Headers are not required, but recommended.
All columns can be imported but this is not mandatory. In many cases the file contains information not relevant for the analysis, so a column selection process allow visualization of only the important parts. The columns selected for import are referred to as the Paramaters.
Some specific features for the mapping of result files are explained in greater details below.
A single result file can contain data for more than one plate. In this case, a column indicating the plate name is recommended. Note that this is not mandatory: an automatic plate numbering is perfomed by PlateEditor based on the number of times the same well name is found in the file. See below for more information.

After being loaded and validated, results can be visualized in the form of heatmaps in the Data Panel, which will display heatmaps for the file, parameters and plate currently selected. Specific controls are available for plate browsing and tuning of the visualization.

Plate View (1)
This control allow browsing of the plates available within the selected result file. Description of the controls, from left to right:
- Display the first plate available
- Display previous plate
- Selection of a plate directly from the drop-down list
- Lookup tool to search specific plate names; start typing to see how many results match you search. Press enter to loop through the matched items
- Display the next plate
- Display the last plate available

Pairing (2)
Information about the definition plates currently paired to the selected result plate will be displayed here. Click the gear icon to access the pairing form and edit the pairing data. See the [Pairing] page for more information.

Linked Layer (3)
This control indicates which layer of the layout is used to display information on the tool-tip that display when the mouse cursor hovers the heatmap.
Layer browsing can be done using the controls as defined above for the plate view

Heatmap (4)
These controls allow tuning of the colors used for the heatmap.
Heatmaps are displayed as 3-color gradients, with the smallest value using the color defined by 0, the average value using the color defined by 50, and the highest value using the color defined by 100.
a. Click on a color to choose among a list of other available options.
b. Click here to choose among a list of available templates

Click on a template to apply the pre-selected colors to your gradient. Use the Invert button to invert the 0-color with the 100-color.

Min & Max (5)
This controls the scope of the minimum and maximum values used to normalize the values and build the heatmaps. Three choices are available:
- Global (default): uses the minimum and maximum values found for the entire result file, i.e. accross all the plates available
- Plate: uses the minimum and maximum values found for the current plate only (local extremums)
- Custom: allow the user to specify the minimum and maximum value to use for the heatmap. Currently applies to all the parameters selected, but will soon be updated to work at the parameter level: the min/max values will thus be customizable for each parameter.

Data panel (6)
The heatmaps for the parameters (selected columns) will appear here.
a. Click on the tab header to show/hide the corresponding heatmap. Click on the trashbin icon to remove this parameter from the list of selected column and delete the corresponding heatmap. The parameter can be selected again using the Edit button of the [Menu Panel].
b. Buttons for export of the heatmaps:
- jpg: create a fixed jpeg image version of the heatmap and display it in a new page. The image can be copy/pasted or saved in your hard-disk.
- html: display an html version of the heatmap (as a table), with the values parsed from the file indicated in each well.
- txt: create a tab-separated .txt file for download; the file contains both the values and normalized values, in a matrix (heatmap) format.

Mapping and validation of result files

Mapping
In essence, mapping can be done as explained on the [Data Import] page, but there are a few specific points requiring additional comments for the results.

• Import (1)
  In this column, tick all the parameters that should be imported for visualization by PlateEditor. This table will lists all the column headers that were parsed from the file.
  At least one paramater should be selected, but there are no restrictions in the maximum number of parameters. Use the shortcuts "All / None" to select all columns available or reset the selection.

• Numeric (2)
  This is used to indicate to PlateEditor when a column contains numerical data, or when it contains textual data.
  If a parameter is imported as text, the heatmap colors will not be applied and the textual value indicated in the well, using the space available (long text will be shrinked to fit the space).
  For parameters labeled as numeric, heatmap colors will be applied, but textual values will be excluded (including the Infinity keyword).
  Columns will be automatically guessed as textual/numeric using the data contained in the first row. Any valid numerical value will assign the parameter as numerical. The user can still adjust this manually to match the desired outcome.

Result validation
When the mapping is completed, result files will be submitted to a validation step. The entire file will be parsed using the configuration selected by the user to count the number of valid wells and enumerate the plates available in the file.
Validation will succeed if at least one valid well entry is found, otherwise it will fail and the heatmaps will not be displayed.
Validation status of a file is indicated by an icon in the result table of the [Menu Panel].

A green tick mark indicates that the result file is validated and the heatmaps will display when selecting this result.
A red cross indicates that the validation failed, or is yet to be performed. Selecting this file will start the validation process and allow the user to navigate back to the mapping and parsing configuration to update these settings if needed.

Strategies for the resolution of plate name
Plate names are gathered from the file during the valiadation process. The resolution will differ depending on the mapping configuration for the result file:

Columns mapped	Rule
Well ID	The plate name is assigned automatically as j, where j is the j-th occurrence of the well ID
Well ID & Plate ID	The plate name is read directly from the column mapped as Plate ID