After collecting and uploading trait data, breeders have to must evaluate them and look for probable outliers and questionable data before sending them for analysis. The Phenotypic Data Manager allows breeders you to:
View, filter, and sort plot data;
View the descriptive statistics of all numeric traits of the active occurrence;
Detect possible outliers;
Suppress and unsuppress unsuppressed plot data; and
Generate box plots, histograms, scatter plots, and heatmaps per trait.
Get started
There are two ways of accessing the Phenotypic Data Manager tool : through the Experiment Manager in tool and the Core Breeding Analytics domain.
Let’s get started!
Get Started
1. From the Experiment Manager browser, select the occurrence for phenotypic data review by ticking the checkbox
on the leftmost column. Note that the occurrence should | Info | |||||
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Reminder:
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and
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On the Experiment Manager browser, tick the checkbox (
) parallel to the selected occurrence. On the upper right of the table, click the Access Breeding Tool button (
) then select Phenotypic Data Manager from the
3. dropdown menu.
| Expand | ||
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You will be redirected to the Phenotypic Data Manager page
which displays the trait data from the selected occurrence. Table, Box Plot, Histogram, Scatter Plot, and Heatmap tabs are available to visualize more about the occurrence. To know more about the tabs, you may check generate visualizations.
However, you may still switch to another occurrence by clicking the dropdown menu.
The Phenotypic Data Manager browser will display the list of all experiments under yourprogram with their experiment types and statuses. To select the occurrence for evaluating trait data, click the Expand button (>) beside the experiment.
Once you have the occurrence in mind, click the radio button (
) on the left side of the occurrence and click Explore from the upper right corner of the browser.
Navigate the Phenotypic Data Manager
The Phenotypic Data Manager tool allows users to view, sort, and verify the data uploaded to your occurrence.
Let’s look at the action items and their functions on the page.
PDM Data Browser
Some occurrences with no plot trait data might be available on this data browser. This is due to data issues in the tool. While these occurrences can be selected on the data browser, they cannot be opened because there is no plot trait data to show.
To resolve this, please let us know by reporting the issue as a bug as soon as you encounter it.
1. Explore button
Component | Name | Function | |
|---|---|---|---|
| 1 |  | Explore | The main button for users to proceed with quality-checking their data in the Phenotypic Data Manager. |
2. Expand All/Collapse All
Component | Name | Function | |
|---|---|---|---|
| 1 |  | Expand All | Shows all the occurrences per experiment in the data browser. |
| 2 |  | Collapse All | Hides all the occurrences in the data browser. Only the experiment names are displayed. |
3. Data Columns and Filters
Component | Name | Function | |
|---|---|---|---|
| 1 |  | Data Column | Displays the data type each column. Users can click on one of these columns to sort the data in ascending or descending order. |
| 2 |   | Search | Searches and filters specific data that the users want to see. They can click the remove filter ( |
4. Experiment and Occurrence
Component | Name | Function | |
|---|---|---|---|
| 1 |  | Experiment name | Displays the experiment name. Users can click the dropdown button beside the experiment name to see the occurrences under it. |
| 2 |  | Occurrence | Displays the occurrences under a certain experiment and their relevant data. Users can also see the status of the occurrence. To select the occurrence for quality-checking, click the radio button ( |
5. Pagination
Component | Name | Function | |
|---|---|---|---|
| 1 |  | Go to page | Located at the bottom left side of the trait table, it allows the user which page to go to view |
| 2 |  | Rows per page | Located at the bottom right side of the trait table, this drop down button allows user to selected number of rows to view per page |
Quality Control
1. Analyze button
Component | Name | Function | |
|---|---|---|---|
| 1 |  | Analyze | The main button for users to send their quality-checked trait data for single-occcurrence analysis. |
2. Select Occurrence
Component | Name | Function | |
|---|---|---|---|
| 1 |  | Select occurrence | Allows user to select which occurrence to view by using the dropdown box. |
3. Main tabs
Component | Name | Function | |
|---|---|---|---|
| 1 |  | Table | View the stats table of the data |
| 2 |  | Box Plot | Visualize data in the form of box plots |
| 3 |  | Histogram | View data in the form of histograms |
| 4 |  | Scatter Plot | Visualize data in the form of scatter plots |
| 5 |  | Heatmap | View data in the form of heat maps |
4. Key Columns and Cells
Component | Name | Function | |
|---|---|---|---|
| 1 |  | Quality Controlled | trait data columns for all plots are checked for quality control |
| 2 |  | Not Quality Controlled | trait data columns for all plots are for review |
| 3 |  | Possible Outliers | trait data identified as outliers based on 1.5 IQR in the trait table. The cell is colored orange. |
| 4 |  | Suppressed Data | trait data identified by users as suppressed. The cell is colored gray. |
| 5 |  | Bad Data | trait data identified as invalid. It may be data that do not conform with the set data type or are not within the set range of values. The cell is colored red. |
| 6 |  | Missing Data | missing data during collection. The cell is empty and colored blue |
5. View Traits
Component | Name | Function | |
|---|---|---|---|
| 1 |  | Trait(s) | A drop down button on the top left of the trait table. The user selects the trait columns to view. |
| 2 |  | Pin/Unpin | Allows users to freeze and unfreeze the first few columns of the trait table. It eases the viewing of trait data without scrolling past the columns. |
6. Main Toolbar
Component | Name | Function | |
|---|---|---|---|
| 1 |  | Comments | This icon, when hovered, displays the comments the user inputs while saving the transanction. |
| 2 |  | Check for updates | This button allows user to check for any updates made to the trait values of the selected occurrence |
| 3 |  | Edit | Edit button allows the user to do trait(s) changes by suppressing, changing the QC code, or resetting to last saved |
| 4 |  | Filter | User can filter to show possible outliers only or suppressed data only or both |
| 5 |  | Save | Used to save the transaction and mark the trait(s) as quality checked |
| 6 |  | Settings | This is the settings button for the trait table |
| 7 |  | Refresh | This button allows user to refresh the trait table |
7. Trait Table columns
Component | Name | Function | |
|---|---|---|---|
| 1 |  | Data Column | Displays the data type each column. Users can click on one of these columns to sort the data in ascending or descending order. |
| 2 |   | Search | Searches and filters specific data that the users want to see. They can click the remove filter ( |
8. Pagination
Component | Name | Function | |
|---|---|---|---|
| 1 | | Go to page | Located at the bottom left side of the trait table, it allows the user which page to go to view |
| 2 | | Rows per page | Located at the bottom right side of the trait table, this drop down button allows user to selected number of rows to view per page |
Great job!Now that you are familiar with the Phenotypic Data Manager browser, you can now start evaluating your trait data.