This section describes all the general panels used in the abundance apps.

Sample Selector

Samples can be selected wih the help of “Sample selector” panel located on the left side of the 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. Load, Save, and delete your current set of modifications with the help of the “settings” button. Users can save their modifier selection with a name of their choice in the “Type a name” box.

• It also consists of the option to Return to your initial set of modifications and 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.
• 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.

Plot Navigation panel

This panel provides users with options to navigate through the plots in the apps.

1. Plot Type lets you select plot types to visualize your data:

• Boxplot – Summarizes the distribution of data with median, quartiles, and whiskers.
• Jitter Plot – Displays individual data points for better visibility of variation.
• Violin Plot – Combines boxplot with kernel density to show data distribution.

2. Plot Options: Users can choose from multiple plot types from the Plot type option for visualizing sequencing quality metrics such as Boxplot, Jitter Plot and Violin Plot

With the help of Group By or Sort by option, users can group their visualization according to the various metadata variables such as “Plate, Tissue, Timepoint,etc”

A settings panel allows users to select or deselect QC parameters to display in the plots. Currently, only Q30 is available for “Sequence tab”, but additional parameters may be added in the future.

3. Quality Indicators lets you choose which alignment parameters to display in the plots (e.g., Number of input reads, Uniquely mapped reads, Average mapped length)

4. Plot Design and Features:

• Each QC parameter is displayed in a separate plot to ensure proper visualization of thresholds.
• Y-axis: Represents the parameter values (e.g., Q30). - Scales are parameter-specific and automatically adjusted based on thresholds, with extra spacing for clarity.
• X-axis: Displays sample groups based on metadata categories (e.g., Tissue, Timepoint, Concentration).
• All samples can be displayed simultaneously by clicking and dragging over it to zoom in, ensuring a detailed overview.
• Users can reset the axes using the small “home” near the plot.

5. Background Color Coding:

• Displays thresholds (if defined in the Threshold Manager) with a semi-transparent color scale for easy interpretation.
• Each plot includes a header with the parameter name.

6. Legend and Hover Details:

• Threshold categories are displayed on hover.
• Metadata group information and highlighted samples are also explained via hover tooltips.

7. Download Options

• The plot can be downloaded using the “camera” icon near the plot.
• A single click allows users to download all plots together for reporting or documentation purposes.

Stats Table panel

This panel provides a detailed tabular view of all the statistical values and key sample identifiers such as “Study, Sample ID, SeqFile (FASTQ file name)” for the parameters with regards to each app.

On clicking the “hamburger icon” above the table, you will be povided with the following options:

• Columns: You can select and deselect the columns you want to explore
• Download CSV: You can download the table in CSV format
• Download XLSX: You can download the table in excel format
• Copy filtered rows: You can copy only the rows you have filtered in the table using the filter option, for further analysis.