Terminology 

Data Viewer = - a collection of sheets

Sheet = - view one or more linked plots and controls

Plot = - a visualization

Icon = - invokes modification controls 

Menu = - icons located on the left side of the data viewer

Droppable = piece of - data that can be dragged and dropped 

Target = place - 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 start a new session or revisit a saved session. 

Q- Can I view data from multiple data nodes? 
A- You can view data from different nodes in one sheet, but not in one plot. 

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. Click  in the right corner 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 to blue targets. 

...

To get started in a new data viewer session click New session  or open 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 on the sheet; to onto the sheet. To do this, use New plot or Get data under Setup in the left menu. The menu words descriptions can be shown shown or hidden  as desired. The menu is organized as 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. Icons Multiple icons can be open at the same time, moved around, and are closed by clicking once and their dialogs dragged around the screen as desired. Close the dialog by clicking the  in the right corner. 

• Common controls include: Save Image Removedwhich will
  Image AddedSave - overwrite a saved session and
  Image Added Save as Image Removedwhich will - save a new session but must be given using a new name, Undo Image Removedand Redo Image Removed which recovers backwards and forwards actions, and Export image Image Removedand Send to notebook Image Removed where
  Image Added Undo - recover backward actions
  Image Added Redo - recover forward actions
  Image Added Export image - download one plot of all plots in a view to your computer
  Image Added Send to notebook - save an image of the entire sheet (all of the plots in view) can be saved or sent to the notebook. 
  
  
• Setup includes: New plot 
   and Get data Image Removedwhich are the  New plot - icons used to make a new plot and navigate
  Image Added Get data - select data from the analysis pipeline.

• Tools include:
  Image Added Select & FilterImage Removed  to filter - make selections and filter selections, Classify Image Removedto filter 
  Image AddedClassify - modify and apply selections as classifications, and Additional actions Image Removed to classifications 
  Image Added Additional actions - create a feature list. list 
  
  
• Configure icons are context-sensitive and available options will change according to the plot type and will also update for each plot prior to closing the icon. Please selected. Please navigate to the Configure help section below for more details. 

...

To make a new plot in the data Data viewer, use the Setup icons.

...

Image AddedNew plot - Clicking a plot type will suggest appropriate data options from results available in the analysis pipeline, then click the node of interest to add it to the sheet. Alternatively, drag and drop the plot to the sheet and continue with any additional selections. 

...

Image AddedGet data - Choosing data will suggest appropriate plot types once 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 it can be placed on the Top, Right, Bottom, Left, or Replace the existing heatmap. Once dropped

...

, a plot type must be chosen. 

                Image Modified

Can you have multiple plots on the sheet?

Yes, build them together. 

• All of the plots are interactive. 
• All of the plots are from the same data project. 
• Selection (on the right side of individual plots and in the menu ) and filtering options are linked for the plots on the sheet. Clear filters in the Select & Filter  mode to remove selections. 
• Save plots together from the menu  or independently within each plot . 

...

• Each plot has its own window ; plot windows can which can be resized by dragging the edge of the plot. 
• Click a plot window to make it active (a dark gray border will appear for the window); the . The Configure icons will show settings for the active plot. 
• When more than one plot is open on a sheet, plots can be rearranged by dragging from one position to another , duplicated , enter full screen, and exit full screen. 
• If multiple plot types are selected together with ctrl-click or shift-click, only the plot configuration controls that are shared will be available to for use. 
• Image Added Select & Filter Image Removed applies Filter - applies to all of the plots on the sheet. 
• Controls are located in the same place for each plot, either in the menu on the left, the top of the plot, or the right side of the plot. Even though each plot type has its own available controls that will vary, common controls such as those available above Setup in the menu:  Save , Save as , Undo , Redo , Export image ,and To notebook , and and 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, and Remove plot  will remain the same. 

...

Why does some data light up green when I hover over it? 

Any data that lights up with highlighted in a green background  when hovered over can be dragged , and dropped onto a blue target .

• This includes legend, axis titles, criteria used in Select & Filter, and table features in tables. Any data present in Plot data will light up green to be highlighted in green and can be dragged to make a plot.  
• Drag and drop manipulation is also possible for data nodes present in the configure icons (e.g. Axes and Style).

...

Yes, report results such as those generated from during differential analysis can be navigated to accessed in the data viewer and specific genes can be plotted. 

• The tables must be plotted on the sheet. One way to do this is to choose New plot , select Table  (only data in table format are available), and select then the data of interest to plot. Features (green with hover) are now available for to drag and drop to drop on the plot type of interest. 

...

• Selections can be made directly on the plot  . This can include selecting populations of cells or selecting genes of interest (e.g. to classify clusters of cells). The menu must still be used to filter , classify , and create gene lists  after in-plot selection. 
• Clicking on the Legend will invoke configure options. The configure options invoked will vary depending on the plot type. 
• Clicking the axis titles will invoke the axes configuration. 

Setup 

New plot Image RemovedImage Added New plot

• Click a plot type. Choosing a plot type will suggest appropriate data options from results available in the analysis pipeline. The search bar can be used to navigate to a specific node of interest (e.g. normalized). Select a data node to add it to the sheet. 
• Alternatively, drag and drop the plot to the sheet (blue targets) and continue with any additional selections.  

•          

Get Data Image Modified Get Data

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 nodes and droppables. 

• Find the data node by expanding the pipeline or use the Search bar to quickly locate results. 

• To create a plot, drag the node to the sheet and continue with additional selections. 
• Recently used (right side) data is organized according to the node from which it is derived and will update according to recent use. If the data viewer session is saved, recently used will be saved.
• Click a node under All data to search data found within that node such as attributes, genes, or lists. Drag data (green droppable) to blue targets (e.g. search the normalized counts node for a gene then drag the gene to color a tSNE plot). Numeric attribute names (e.g # cells) are green while categorical attribute names (e.g. classifications) are blue. 

Tools

Image Added Select & Filter Image RemovedFilter

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. 

...

Classify  Image Removed Image Added Classify

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 new classification. Classification names can be edited and the Classifications can be deleted. The number of points in the classification are listed and will be updated accordingly with any changes. Classify selection requires a label (name) and will overwrite the previous applied classification if the points have already been classified. Apply classifications can be used to apply the classification to a data node. 

Additional actions Image Modified Additional actions

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. Open as many icons as you need and move them around the screen then click  in the right corner to close the icon when finished. Changes will automatically be saved before closing and will not affect other plots unless both windows are selected and modified together. If an icon is opened from a plot and kept on the screen but not available for use in a different type of plot, you will be notified that the configuration is not available for the selected plot. 

Description Image Modified Description

• Click the Title on a plot or choose the Description icon from the menu. 
• This contains Title and Legend settings. 

Axes Image Modified Axes

• Click the Axes icon from the menu. The axes dialogue can also be opened by clicking the X, Y, or Z axis titles. 
• The available options change depending on the plot type. 
• Features and attributes can be dragged to the Axes card . Alternatively, drag feature and attributes from the axis to plots using the data node . 

Data Image Modified Data

• Data configuration options frequently change for different plot types. See the examples below. 

Style Image Modified Style

• Style can be invoked from the menu or by clicking the Legend of most plot types. 
• This is where Color, Size, Shape, Labeling, and Style (bar or line) settings are found. 

Grouping Image Modified Grouping

• Grouping is only invoked from the menu. 
• This is where you split, connect, and highlight by data. 

Statistics Image Modified Statistics

• Statistics is invoked in the menu. 
• It is used for Analytics (regression line) and to modify plot Significance. 

Background Image Modified Background

• The Background can be modified for some ploy types; this setting is found in the menu. 
• PNG, JPG, and BMP files are supported by all major web browsers. Your browser may support additional formats. 

Control Image Modified Control 

• Control is used for 3D scatter plots and found in the menu. 
• This is where settings for moving the 3D plot are found. 

...