With the plot overview page you easily be able to navigate through all the plots saved within the track. Furthermore the page will also provide you the possibility to create new plots and browse through the details of selected plots. Using the search plot option you will also be able to directly navigate to your plot of preference after which you can interactively view the plot of choice. 

TABLE OF CONTENTS

• 1. Opening the track
• 2. Navigating the plot overview page
• 3. Plot banners
• 4. Viewing a plot

1. Opening the track

To get to Plot overview page the user should click the "Open" button under the track of choice. The user will then be redirected to the plots saved within the track. 

2. Navigating the plot overview page

Once you open the track you will see the overview shown above. Various plots saved within the track can be navigated through this page. On the left side you see the enlarged version of the selected plot, under it you can see the plot details. By default the first plot of the track is selected. On the right side you see the ordered plots in the current track.

The following features are accessible within the plot overview page: 

• Create new plot: By clicking on create plot to the top right, the project page a new analysis can be run
• Search plots: The search plot filed located on the top right can be used to easily navigate to plots of choice.
• Select plots: Once the plot is located you can select the plot by clicking on the "select button" under the preferred plot. Once the plot is selected, the plot will appear in focus on to right side of the screen. 
• Details: If the plot is not already selected the details of the plot can be visualised by clicking on the "details" button located under the preview thumbnail of the plot. In the case that the plot is selected and magnified to the right, the plot details are visible in the field under the view interactively section. 
• View Interactively: Allows the user to navigate and visualise the plot interactively.

3. Plot banners

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Each plot thumbnail has a banner running across the top-right corner indicating either the status of the algorithm creating the plot or the type of plot. There are six different types:

• Placeholder banner - when a plot is first created, it has a dark red 'Placeholder' banner. The placeholder banner indicates that the algorithm behind the plot has not been run yet. The create plot quick link on the landing page links to the most recently created placeholder plot
  
• Running banner - When an algorithm is running but has not yet completed, the 'Placeholder' banner is replaced with a light blue 'Running' banner
  
• Interactive banner - after the algorithm finishes running, a green 'Interactive' banner replaces the 'Running' banner if the plot is interactive
  
• Static Image banner - after the algorithm finishes running, a dark blue 'Static' banner replaces the 'Running' banner if the plot is not interactive
  
• Process Error banner - an error caused the algorithm to fail, producing no plot.
• Merged banner - the output of the "Merge" module
• Integrated banner - the output of the "scRNA-seq data integration" module
• Engineered banner - the output of the "Gene set variation analysis" module

The plots with the Merged, Integrated and Engineered banners are the output of modules that perform some sort of modification to the data matrix of the input dataset. They do not have an interactive plot page, but can be used as input for other modules.

4. Viewing a plot

Selecting a plot brings up a larger thumbnail and the details of the selected plot. Clicking on the Plot details button will bring up a new window to edit the details of the plot. If the plot is interactive, clicking on the View interactively button will bring up an interactive view of an the plot. For more information you can read the chapter on the Interactive plot page. If it is not interactive, the View interactively button will be not be displayed.

Under the enlarged plot you can read the plot name and description. By clicking on the "Show analysis step history" button the analysis history of the previous six analysis steps will be displayed with the settings used to perform these analyses. 

Clicking on the "Hide analysis step history" will hide the displayed analysis step history.