Data Viewer
Data Viewer
Terminology
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
FAQs
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- 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.
How do I get started and navigate the data viewer?
Configure icons are context-sensitive and available options will change according to the plot type selected. Please navigate to the Configure help section below for more details.
How do I make a plot?
To make a new plot in the Data viewer, use the Setup icons.
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.
Can you have multiple plots on the sheet?
Yes, build them together.
All plots are interactive.
All plots are from the same data project.
When there are multiple plots, how are they controlled and configured?
Each plot has its own window that can be resized by dragging the edge of the plot.
Click a plot window to make it active (a dark gray border will appear around the window when active). The Configure icons display settings for the active plot.
My screen is full of plots. How do I add more plots without starting a new data viewer session?
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).
Why does some data highlight in green when I hover over it?
This includes legend, axis titles, criteria used in Select & Filter, and table features. Any data present in Plot data will be highlighted in green and can be dragged to make a plot.
How do I color my plot by a gene?
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.
Drag and drop the gene of interest from the appropriate node in Get data (e.g., normalized counts). The Recently used list can be helpful for this if you have already recently used the gene.
Drag and drop features from another plot on the sheet (e.g., an axis title from a violin plot) or drag and drop features from criteria added to the Select & Filter icon.
Can I plot genes from tables without going back to the analysis pipeline?
Yes, report results such as those generated during differential analysis can be accessed in the data viewer and specific genes can be plotted.
How do I manipulate my plot without using Tools or Configure?
Setup
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 a plot onto the sheet and drop it on a blue target, then continue with your selections.
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.
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
Deselected points (the points that are not selected) can either be Dim (colors are not as bright) or Gray (not colored but instead gray)
There are two selection modes: Manual and Criteria.
Manual
Criteria
Data can be dragged directly to Add criteria to generate selections or use the drop-down.
Selections can be dragged to blue targets.
Each criterion can be modified. Invert can be used to include or exclude selections. When modifying criteria by low or high values, pin histogram lets you see multiple histograms at a time. Histograms are colored according to selections; dark blue is the current selection, gray is data outside the current selection (i.e. the positions of the slider handles), and light blue is data that is within the slider’s selected region but is currently deselected by other criteria.
Filter Click:
The Apply observation filter and Apply feature filter are used to apply filters to data nodes in the analysis pipeline.
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".
Filter Click:
The Apply observation filter and Apply feature filter are used to apply filters to data nodes in the analysis pipeline.
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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.
Configure
Click the Title on a plot or choose the Description icon from the menu.
This contains Title and Legend settings.
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.
Transpose the axis.
Modify the plotted Content (the data represented).
Alter the Grid and Sorting settings.
Content configuration options are available for tables and text where it contains modification options as well as the node where the data comes from in the analysis pipeline; to change this source select the node of interest by clicking on it.
Style can be invoked from the menu or by clicking the Legend on most plot types.
Color, Size, Shape, Labeling, Summary (e.g. violin), and Style (bar or line) settings are accessed using this icon.
Grouping is only invoked from the menu.
Access split, connect, and highlight by options.
Statistics are invoked in the menu.
Used for Analytics (regression line) and to modify plot Significance.
The Background can be modified for some plot 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 is used for 3D scatter plots and found in this menu.
Settings for moving the 3D plot.
Heatmap & Bubble map
Please see Hierarchical Clustering Configuration Settings for details related to configuring a heatmap or bubble map in the data viewer.
Additional Assistance
If you need additional assistance, please visit our support page to submit a help ticket or find phone numbers for regional support.
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