Data Viewer - a collection of sheets
Sheet - one or more linked plots and controls
Plot - a visualization
Icon - graphical representation of tools or controls
Panel (menu) - Collection of tools and options available for user selection
Droppable - data that can be dragged and dropped
Target - location to drop a droppable
Node - data results from the analysis pipeline
Q- What is the Data Viewer?
A - The Data viewer is a general-purpose data visualization tool that includes 2D and 3D scatter plots, histograms, heatmaps, violin plots, and more.
Q- How is it invoked?
A- Select a data node and double-click to view the task results in the Data viewer. You can also select the Data viewer tab in a project to either start a new session or revisit a saved session.
Q- Can I open more than one icon at a time and move it around?
A- Yes, open as many icons as you need at a time and move them around the screen. Either click in the right corner to close the icon or click on the icon in the menu again to close the icon.
Q- Is there a recently used function?
A- Yes, there is a recently used function within the Get data icon. This lets you drag recent nodes or the green droppables (data within a node) to blue targets.
To get started in a new data viewer session click New session or open a previously saved session. Clicking New session will prompt you to drag and drop an available plot or data node to visualize your data onto the sheet. To do this, use New plot or Get data under Setup in the left menu. The menu descriptions can be shown or hidden as desired. The menu is organized into single-click Common Controls, Setup, Tools, and Configure icons. Common controls and Setup icons do not change but Tools and Configure icons are context-sensitive and will change according to the selected plot type. Multiple icons can be open at once and their dialogs dragged around the screen as desired. Close the dialog by clicking the in the right corner or by clicking on the icon again in the menu.
To make a new plot in the Data viewer, use the Setup icons.
New plot - Clicking to choose a plot type will suggest any appropriate data options from the results that are available in the analysis pipeline, click a node of interest to add it to the sheet.
Get data - The data type chosen controls which plots will be available for use after the data is dragged onto the sheet. Note that All data nodes (left) follow the hierarchy used in the analysis pipeline while Recently used (right) nodes are updated according to recent use and can similarly be used to plot data.
Note the target locations presented in blue (top, bottom, left, right, & replace) when dragging data. In this example, a data node chosen from Get data, is being dragged onto the sheet and can be placed at the Top, Right, Bottom, Left, or Replace the existing heatmap. Once dropped on a target location, a plot type must be chosen.
Yes, build them together.
At the left of the plot:
Save
Save a
Undo
Redo
Export image
To notebook
Capture video
At the top of the plot:
Hide controls
Show controls
Click and drag to move the plot
Duplicate
Export image
Send to notebook
Enter Full screen,
Exit Full screen
Remove plot
Multiple sheets (where plots are added) are allowed in the data viewer. This is helpful when you cannot fit more plots on the sheet (screen), but you still want to use all of the settings that you are working with (e.g., recently used).
Any data highlighted in a green background when hovered over can be dragged and dropped onto a blue target .
There are multiple ways to color plots by a gene or protein (feature) of interest. You can also color by more than one feature on the same plot or even feature lists. You can also choose to represent a feature with styles other than color, like shape or size.
Yes, report results such as those generated during differential analysis can be accessed in the data viewer and specific genes can be plotted.
All data results from building the analysis pipeline are found here. This icon is used to create plots, to plot attributes and features of interest (e.g., color a plot by a gene of interest from the normalized data node), and to plot Recently used data.
Find the data node by expanding the pipeline or use the Search bar to quickly locate results.
This icon is where selections are made (left side) and filtered (right side). Selecting and filtering will be applied to all plots in the sheet. Selections can be used to filter and/or classify . Selections used to filter can be named under classify and indicate the number of cells included.
The Classify icon holds draft classifications to be applied or saved classifications that can be opened, applied, and refined as necessary then saved again as a classification with a new name. Classification names can be edited, and the Classifications can be deleted. The number of points in the classification are listed and will be updated in accordance with any changes. Classify selection requires a label (name) and will overwrite any previously applied classification. Apply classifications can be used to apply the classification to the project. We recommend frequently saving the data viewer session while classifying cells, prior to applying the classifications; any classifications that have been made but not applied can be viewed on plots using "New classification".
The Additional actions icon holds other available plot actions. This icon will become available for applicable plot types (e.g., heatmap). Currently, it is used to Create a feature list.
These are the configuration options for plots under Configure. Each of the below icons open a dialog box with plot configuration options. Dialogs can be dragged anywhere on the screen and remain open until closed by clicking in the upper right corner of the dialog. Multiple dialogs can be open at once. Changes are auto saved and do not affect other plots unless both plots are selected and modified together. If a dialog is open but is not available for use in the currently selected plot, a warning will appear.
Please see Hierarchical Clustering Configuration Settings for details related to configuring a heatmap or bubble map in the data viewer.