Sample Selector

Sample Selector panel

Samples can be selected wih the help of “Sample selector” panel located on the left side of the app interface.

This panel provides a variety of filters under the operation called “Modifiers”, that can be used to narrow down the samples selected from the entire catalogue of samples in your project to the ones you are interested in. For QC purposes it is usually advisable to start with one complete study to get an overview.

To filter the samples, modifier(s) need to be added. It is done by adding as many modifiers as required from the drop down menu (See below). An empty value field in a modifier will result in selection of all available data and has no modification effect. Any column in the sample table can be selected for applying modifier (with constraints of type of modifier and value type in the field). Corresponding values should be selected if to be included/excluded in the modification.

Note: For further information on modifier functionality, check modifier tooltip.

Modifiers

A modifier is a filter or enrichment applied on the table columns resulting from last applied modifier. It consists of the following functions:

1. Filter Study is a “mandatory filter” to select and load your studies of interest. Please click on the field below “Values” to select the studies from a drop-down menu.

2. Add a new modifier from the drop-down below and confirm the addition by clicking on the "+" button.

   • Filter categ. can filter the samples according to categorical variables such as " Tissue, Sex, Compound, etc". The values in the selected column of the table will also appear for selection in the values field under this category.
   • Filter num. can filter the samples according to numerical variables. A slider will appear, with range of minimum and maximum numeric value in the column.
   • Join columns can combine two or more categorical variables into one. For e.g., on selecting the categories sex (male, female) and tissue (liver, brain, heart) will result in male_liver, male_brain, male_heart, female_liver, female_brain, female_heart, which can now be used for further filtering or as analysis options within the apps. It produces a new column by joining the values from the columns selected in combine field. It uses underscore for joining levels of the selected columns and names the new column by the given label.
   • Column binning can divide samples into groups according to a specified numeric variable. It produces a new labeled column with bin ID’s given by selected number of bins. Currently it provides two modes and can only work on columns with numerical values.
   • Enrich can add additional information to your sample table, such as “QC Data, Patient data and Custom annotations”
   • Additionally, you can toggle between Include or Exclude to keep the specified values in or out of your selection.

3. The “settings” button on right-side of the + button provides the following options:

   1. Load current modifications to the project
   2. Save the current modification selection with a name of ypur choice in the “Type a name” box.
   3. Delete the current modification selection
   4. Switch between the “globe” and the “person” icon which symbolizes global (project wide) and local (only current user). The former helps saving and loading modifier sets stored for all users and the latter for current users. This will also allow you to make the sample selection in all abundance based apps.
   5. Return to your initial set of modifications

• Show excluded samples displays samples that are marked as excluded. Note: In QC apps the default setting is that all the samples including the excluded ones are shown. For all other apps the default is that excluded samples are not shown.
• Instant mode can be enabled to automatically apply changes as they are made. Disable this option to manually apply changes by clicking the apply button. The double tick icon on the “Apply changes” button indicates that there are unsaved changes waiting to be applied.