Evaluate plot trait data
- Rica Aicel Mariano
View tables
The Table tab has two sections where the Stats and Trait table section allows us to assess the phenotypic data before running the desired analysis.
The Stats section contains the descriptive statistics of all numeric traits of the active occurrence. The table is shown by default, but you may click the dropdown button (
) beside the section title to show or hide the table.
The Trait Table section allows the user to suppress or unsuppress raw data collected per plot, per trait, or per data point.
Before reviewing your plot trait data, you must be familiar with the color-coded keys in the Phenotypic Data Manager. These keys group your data depending on their types and whether the collected trait is quality-checked or not. Any changes to the data will be reflected in the trait table. Click on the dropdown menu for the list of keys.
Column Keys | Cell Keys |
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Pin columns
Pinning the first few columns of your Trait Table lets you view the trait data values without scrolling past the main columns such as the plot and entry numbers, germplasm data, and planting arrangement information.
Click the Pin button above the table to freeze the first column. Repeat this step until you pin the needed columns.
To undo, click Unpin. Repeat this step until the columns are returned to normal.
Sort and filter data
Sort using headers
You may sort your data in ascending or descending order by clicking the column headers.
Filter using the search bar
You can filter your data by typing the specific data in the search bar under each header.
Filter using settings
You may also filter your data by showing only the outliers and/or suppressed data. From the toolbar above the trait table, click the filter icon ().
Click Show possible outliers only, Show suppressed data only, or both by clicking the checkbox () above.
Filter trait columns
You may also select the trait columns that you want to hide or show in your table.
Click the Trait(s) dropdown menu from the upper left part of the table.
Click the trait(s) that you want to view in the table. You may select one or more traits, or click the All traits option. Click again on the trait(s) to deselect.
Once done, click Apply.
Assign trait data classification
Assign QC code of each trait data
You can change the QC code of your plot trait data individually in the Phenotypic Data Manager. Locate a cell in the trait table and right-click to view all the QC codes. The cell will then change color depending on the classification of data. Click the dropdown menu for the options.
Initially, all trait data have the default QC code of Questionable except those with bad and missing data.
When you right-click on trait data with the QC code of bad, suppressed, or questionable, the option to change them to Good or Questionable is disabled if the trait data value follows the data format for that trait. A brief explanation is also provided for your reference.
Change QC code by trait
This allows all data under the selected trait column to change into a specific QC code.
From the toolbar, click Edit and select Change QC code by trait.
Select the trait and the QC code from the modal window to be updated.
Once done, click Update.
All data from the selected trait will be updated with the selected QC code and the cells will change color depending on the QC code.
Suppress multiple trait data
While you can suppress the trait data values individually by changing the QC code, you can also suppress them in bulk. There are three ways of suppressing: (1) by suppressing all possible outliers, (2) by suppressing outliers from a trait column, and (3) by suppressing trait data of selected plots.
Suppress all possible outliers
This allows you to suppress all the outliers automatically identified in the trait table.
From the toolbar above the trait table, click Edit, then Suppress all possible outliers.
A modal window will notify you that you will suppress all the possible outliers. Click Suppress to confirm. When it’s done, the cells with the outliers will change their color to gray.
Suppress possible outliers by trait
This allows you to suppress all the outliers from a specific trait column in the table.
From the toolbar above the trait table, click Edit, then Suppress possible outliers by trait.
A modal window will notify you that you will suppress all the possible outliers of that trait. From there, select the trait where the outliers will be suppressed.
Click Suppress to confirm. When it’s done, the cells with outliers from the selected trait column will change their color to gray.
Suppress from selected plot
This allows you to suppress all the trait data from a specific plot row in the table.
Tick the checkbox () of the plot(s) where you want to suppress data. From the toolbar above the trait table, click Edit, then Suppress possible outliers by trait.
All the data selected will be suppressed and the cells will change their color to gray.
Review trait data
If you need to update your trait data in PDM, either by changing the QC code of a trait data or by updating the data from the Core Breeding domain, you may view these changes in the Phenotypic Data Manager.
Show edit history
Any changes in the QC code of a selected trait data can be viewed by checking its edit history. You must first save all the changes to your trait data before viewing the edit history.
Right-click on the cell with the trait data and select Show edit history.
The pop-up message will display the person who changed the trait QC code, the date and time it was updated, and the replaced QC code of the selected trait data.
You may also check previous and recent changes by clicking the arrows in the pop-up window.
Review updated data from Core Breeding
Any changes to your trait data from the Core Breeding domain can be checked and updated in the Phenotypic Data Manager.
From the Trait Table toolbar, click the Check for Updates button. If no changes were made to your trait data, the button will change to you're up to date.
On the other hand, if the system detects changes in your trait data, the Check for Updates button will change to Update Transaction.
After clicking the Update Transaction button, a modal window will appear to notify you that the current transaction will be closed and a new transaction with the updated changes will be reflected in the table. Click Yes to confirm.
Once done, the browser will refresh with the new transaction and updated trait data.
Save changes
Once done reviewing your trait data, you may finally save it. By saving the changes, the trait data will be marked as good data. There are two ways to do so.
From the toolbar above the trait table, click the save icon ().
One option is that you can Save your QC changes without selecting traits. This will save the changes without marking the traits as QCed.
Marking traits as QCed
Another option is to mark trait data columns with at least one (1) good data and no questionable data as quality-checked (QCed).
Select the trait(s) that are done for quality checking. Optionally, write comments on the textbox provided.
Once done, click Save to confirm. The selected traits will be marked as quality checked (QCed) and will save your QC changes, and the questionable data will be set to GOOD.
By clicking the beside Close Transaction, the system will close the transaction without applying the previous changes. A new transaction will then be made with the most recent trait data from Core Breeding.
After saving, a modal window will appear notifying you of your successful transaction.
The column headers of the QCed traits will change to green.
In the Experiment Manager tool, your occurrence will now have the additional status of trait data quality checked.
Great job! Your phenotypic data has undergone quality checking and is ready for analysis. If you want to review your data thoroughly, you may proceed with generating data visualizations.