Partek
  • Overview
  • Partek Flow
    • Frequently Asked Questions
      • General
      • Visualization
      • Statistics
      • Biological Interpretation
      • How to cite Partek software
    • Quick Start Guide
    • Installation Guide
      • Minimum System Requirements
      • Single Cell Toolkit System Requirements
      • Single Node Installation
      • Single Node Amazon Web Services Deployment
      • Multi-Node Cluster Installation
      • Creating Restricted User Folders within the Partek Flow server
      • Updating Partek Flow
      • Uninstalling Partek Flow
      • Dependencies
      • Docker and Docker-compose
      • Java KeyStore and Certificates
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    • Live Training Event Recordings
      • Bulk RNA-Seq Analysis Training
      • Basic scRNA-Seq Analysis & Visualization Training
      • Advanced scRNA-Seq Data Analysis Training
      • Bulk RNA-Seq and ATAC-Seq Integration Training
      • Spatial Transcriptomics Data Analysis Training
      • scRNA and scATAC Data Integration Training
    • Tutorials
      • Creating and Analyzing a Project
        • Creating a New Project
        • The Metadata Tab
        • The Analyses Tab
        • The Log Tab
        • The Project Settings Tab
        • The Attachments Tab
        • Project Management
        • Importing a GEO / ENA project
      • Bulk RNA-Seq
        • Importing the tutorial data set
        • Adding sample attributes
        • Running pre-alignment QA/QC
        • Trimming bases and filtering reads
        • Aligning to a reference genome
        • Running post-alignment QA/QC
        • Quantifying to an annotation model
        • Filtering features
        • Normalizing counts
        • Exploring the data set with PCA
        • Performing differential expression analysis with DESeq2
        • Viewing DESeq2 results and creating a gene list
        • Viewing a dot plot for a gene
        • Visualizing gene expression in Chromosome view
        • Generating a hierarchical clustering heatmap
        • Performing biological interpretation
        • Saving and running a pipeline
      • Analyzing Single Cell RNA-Seq Data
      • Analyzing CITE-Seq Data
        • Importing Feature Barcoding Data
        • Data Processing
        • Dimensionality Reduction and Clustering
        • Classifying Cells
        • Differentially Expressed Proteins and Genes
      • 10x Genomics Visium Spatial Data Analysis
        • Start with pre-processed Space Ranger output files
        • Start with 10x Genomics Visium fastq files
        • Spatial data analysis steps
        • View tissue images
      • 10x Genomics Xenium Data Analysis
        • Import 10x Genomics Xenium Analyzer output
        • Process Xenium data
        • Perform Exploratory analysis
        • Make comparisons using Compute biomarkers and Biological interpretation
      • Single Cell RNA-Seq Analysis (Multiple Samples)
        • Getting started with the tutorial data set
        • Classify cells from multiple samples using t-SNE
        • Compare expression between cell types with multiple samples
      • Analyzing Single Cell ATAC-Seq data
      • Analyzing Illumina Infinium Methylation array data
      • NanoString CosMx Tutorial
        • Importing CosMx data
        • QA/QC, data processing, and dimension reduction
        • Cell typing
        • Classify subpopulations & differential expression analysis
    • User Manual
      • Interface
      • Importing Data
        • SFTP File Transfer Instructions
        • Import single cell data
        • Importing 10x Genomics Matrix Files
        • Importing and Demultiplexing Illumina BCL Files
        • Partek Flow Uploader for Ion Torrent
        • Importing 10x Genomics .bcl Files
        • Import a GEO / ENA project
      • Task Menu
        • Task actions
        • Data summary report
        • QA/QC
          • Pre-alignment QA/QC
          • ERCC Assessment
          • Post-alignment QA/QC
          • Coverage Report
          • Validate Variants
          • Feature distribution
          • Single-cell QA/QC
          • Cell barcode QA/QC
        • Pre-alignment tools
          • Trim bases
          • Trim adapters
          • Filter reads
          • Trim tags
        • Post-alignment tools
          • Filter alignments
          • Convert alignments to unaligned reads
          • Combine alignments
          • Deduplicate UMIs
          • Downscale alignments
        • Annotation/Metadata
          • Annotate cells
          • Annotation report
          • Publish cell attributes to project
          • Attribute report
          • Annotate Visium image
        • Pre-analysis tools
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        • Quantification
          • Quantify to annotation model (Partek E/M)
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          • Quantify to reference (Partek E/M)
          • Quantify regions
          • HTSeq
          • Count feature barcodes
          • Salmon
        • Filtering
          • Filter features
          • Filter groups (samples or cells)
          • Filter barcodes
          • Split by attribute
          • Downsample Cells
        • Normalization and scaling
          • Impute low expression
          • Impute missing values
          • Normalization
          • Normalize to baseline
          • Normalize to housekeeping genes
          • Scran deconvolution
          • SCTransform
          • TF-IDF normalization
        • Batch removal
          • General linear model
          • Harmony
          • Seurat3 integration
        • Differential Analysis
          • GSA
          • ANOVA/LIMMA-trend/LIMMA-voom
          • Kruskal-Wallis
          • Detect alt-splicing (ANOVA)
          • DESeq2(R) vs DESeq2
          • Hurdle model
          • Compute biomarkers
          • Transcript Expression Analysis - Cuffdiff
          • Troubleshooting
        • Survival Analysis with Cox regression and Kaplan-Meier analysis - Partek Flow
        • Exploratory Analysis
          • Graph-based Clustering
          • K-means Clustering
          • Compare Clusters
          • PCA
          • t-SNE
          • UMAP
          • Hierarchical Clustering
          • AUCell
          • Find multimodal neighbors
          • SVD
          • CellPhoneDB
        • Trajectory Analysis
          • Trajectory Analysis (Monocle 2)
          • Trajectory Analysis (Monocle 3)
        • Variant Callers
          • SAMtools
          • FreeBayes
          • LoFreq
        • Variant Analysis
          • Fusion Gene Detection
          • Annotate Variants
          • Annotate Variants (SnpEff)
          • Annotate Variants (VEP)
          • Filter Variants
          • Summarize Cohort Mutations
          • Combine Variants
        • Copy Number Analysis (CNVkit)
        • Peak Callers (MACS2)
        • Peak analysis
          • Annotate Peaks
          • Filter peaks
          • Promoter sum matrix
        • Motif Detection
        • Metagenomics
          • Kraken
          • Alpha & beta diversity
          • Choose taxonomic level
        • 10x Genomics
          • Cell Ranger - Gene Expression
          • Cell Ranger - ATAC
          • Space Ranger
          • STARsolo
        • V(D)J Analysis
        • Biological Interpretation
          • Gene Set Enrichment
          • GSEA
        • Correlation
          • Correlation analysis
          • Sample Correlation
          • Similarity matrix
        • Export
        • Classification
        • Feature linkage analysis
      • Data Viewer
      • Visualizations
        • Chromosome View
          • Launching the Chromosome View
          • Navigating Through the View
          • Selecting Data Tracks for Visualization
          • Visualizing the Results Using Data Tracks
          • Annotating the Results
          • Customizing the View
        • Dot Plot
        • Volcano Plot
        • List Generator (Venn Diagram)
        • Sankey Plot
        • Transcription Start Site (TSS) Plot
        • Sources of variation plot
        • Interaction Plots
        • Correlation Plot
        • Pie Chart
        • Histograms
        • Heatmaps
        • PCA, UMAP and tSNE scatter plots
        • Stacked Violin Plot
      • Pipelines
        • Making a Pipeline
        • Running a Pipeline
        • Downloading and Sharing a Pipeline
        • Previewing a Pipeline
        • Deleting a Pipeline
        • Importing a Pipeline
      • Large File Viewer
      • Settings
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        • Components
          • Filter Management
          • Library File Management
            • Library File Management Settings
            • Library File Management Page
            • Selecting an Assembly
            • Library Files
            • Update Library Index
            • Creating an Assembly on the Library File Management Page
            • Adding Library Files on the Library File Management Page
            • Adding a Reference Sequence
            • Adding a Cytoband
            • Adding Reference Aligner Indexes
            • Adding a Gene Set
            • Adding a Variant Annotation Database
            • Adding a SnpEff Variant Database
            • Adding a Variant Effect Predictor (VEP) Database
            • Adding an Annotation Model
            • Adding Aligner Indexes Based on an Annotation Model
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          • Usage Report
      • Server Management
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        • System Administrator Guide (Linux)
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        • Moving Data
        • Partek Flow Worker Allocator
      • Enterprise Features and Toolkits
        • REST API
          • REST API Command List
      • Microarray Toolkit
        • Importing Custom Microarrays
      • Glossary
    • Webinars
    • Blog Posts
      • How to select the best single cell quality control thresholds
      • Cellular Differentiation Using Trajectory Analysis & Single Cell RNA-Seq Data
      • Spatial transcriptomics—what’s the big deal and why you should do it
      • Detecting differential gene expression in single cell RNA-Seq analysis
      • Batch remover for single cell data
      • How to perform single cell RNA sequencing: exploratory analysis
      • Single Cell Multiomics Analysis: Strategies for Integration
      • Pathway Analysis: ANOVA vs. Enrichment Analysis
      • Studying Immunotherapy with Multiomics: Simultaneous Measurement of Gene and Protein
      • How to Integrate ChIP-Seq and RNA-Seq Data
      • Enjoy Responsibly!
      • To Boldly Go…
      • Get to Know Your Cell
      • Aliens Among Us: How I Analyzed Non-Model Organism Data in Partek Flow
    • White Papers
      • Understanding Reads in RNA-Seq Analysis
      • RNA-Seq Quantification
      • Gene-specific Analysis
      • Gene Set ANOVA
      • Partek Flow Security
      • Single Cell Scaling
      • UMI Deduplication in Partek Flow
      • Mapping error statistics
    • Release Notes
      • Release Notes Archive - Partek Flow 10
  • Partek Genomics Suite
    • Installation Guide
      • Minimum System Requirements
      • Computer Host ID Retrieval
      • Node Locked Installation
        • Windows Installation
        • Macintosh Installation
      • Floating/Locked Floating Installation
        • Linux Installation
          • FlexNet Installation on Linux
        • Installing FlexNet on Windows
        • License Server FAQ's
        • Client Computer Connection to License Server
      • Uninstalling Partek Genomics Suite
      • Updating to Version 7.0
      • License Types
      • Installation FAQs
    • User Manual
      • Lists
        • Importing a text file list
        • Adding annotations to a gene list
        • Tasks available for a gene list
        • Starting with a list of genomic regions
        • Starting with a list of SNPs
        • Importing a BED file
        • Additional options for lists
      • Annotation
      • Hierarchical Clustering Analysis
      • Gene Ontology ANOVA
        • Implementation Details
        • Configuring the GO ANOVA Dialog
        • Performing GO ANOVA
        • GO ANOVA Output
        • GO ANOVA Visualisations
        • Recommended Filters
      • Visualizations
        • Dot Plot
        • Profile Plot
        • XY Plot / Bar Chart
        • Volcano Plot
        • Scatter Plot and MA Plot
        • Sort Rows by Prototype
        • Manhattan Plot
        • Violin Plot
      • Visualizing NGS Data
      • Chromosome View
      • Methylation Workflows
      • Trio/Duo Analysis
      • Association Analysis
      • LOH detection with an allele ratio spreadsheet
      • Import data from Agilent feature extraction software
      • Illumina GenomeStudio Plugin
        • Import gene expression data
        • Import Genotype Data
        • Export CNV data to Illumina GenomeStudio using Partek report plug-in
        • Import data from Illumina GenomeStudio using Partek plug-in
        • Export methylation data to Illumina GenomeStudio using Partek report plug-in
    • Tutorials
      • Gene Expression Analysis
        • Importing Affymetrix CEL files
        • Adding sample information
        • Exploring gene expression data
        • Identifying differentially expressed genes using ANOVA
        • Creating gene lists from ANOVA results
        • Performing hierarchical clustering
        • Adding gene annotations
      • Gene Expression Analysis with Batch Effects
        • Importing the data set
        • Adding an annotation link
        • Exploring the data set with PCA
        • Detect differentially expressed genes with ANOVA
        • Removing batch effects
        • Creating a gene list using the Venn Diagram
        • Hierarchical clustering using a gene list
        • GO enrichment using a gene list
      • Differential Methylation Analysis
        • Import and normalize methylation data
        • Annotate samples
        • Perform data quality analysis and quality control
        • Detect differentially methylated loci
        • Create a marker list
        • Filter loci with the interactive filter
        • Obtain methylation signatures
        • Visualize methylation at each locus
        • Perform gene set and pathway analysis
        • Detect differentially methylated CpG islands
        • Optional: Add UCSC CpG island annotations
        • Optional: Use MethylationEPIC for CNV analysis
        • Optional: Import a Partek Project from Genome Studio
      • Partek Pathway
        • Performing pathway enrichment
        • Analyzing pathway enrichment in Partek Genomics Suite
        • Analyzing pathway enrichment in Partek Pathway
      • Gene Ontology Enrichment
        • Open a zipped project
        • Perform GO enrichment analysis
      • RNA-Seq Analysis
        • Importing aligned reads
        • Adding sample attributes
        • RNA-Seq mRNA quantification
        • Detecting differential expression in RNA-Seq data
        • Creating a gene list with advanced options
        • Visualizing mapped reads with Chromosome View
        • Visualizing differential isoform expression
        • Gene Ontology (GO) Enrichment
        • Analyzing the unexplained regions spreadsheet
      • ChIP-Seq Analysis
        • Importing ChIP-Seq data
        • Quality control for ChIP-Seq samples
        • Detecting peaks and enriched regions in ChIP-Seq data
        • Creating a list of enriched regions
        • Identifying novel and known motifs
        • Finding nearest genomic features
        • Visualizing reads and enriched regions
      • Survival Analysis
        • Kaplan-Meier Survival Analysis
        • Cox Regression Analysis
      • Model Selection Tool
      • Copy Number Analysis
        • Importing Copy Number Data
        • Exploring the data with PCA
        • Creating Copy Number from Allele Intensities
        • Detecting regions with copy number variation
        • Creating a list of regions
        • Finding genes with copy number variation
        • Optional: Additional options for annotating regions
        • Optional: GC wave correction for Affymetrix CEL files
        • Optional: Integrating copy number with LOH and AsCN
      • Loss of Heterozygosity
      • Allele Specific Copy Number
      • Gene Expression - Aging Study
      • miRNA Expression and Integration with Gene Expression
        • Analyze differentially expressed miRNAs
        • Integrate miRNA and Gene Expression data
      • Promoter Tiling Array
      • Human Exon Array
        • Importing Human Exon Array
        • Gene-level Analysis of Exon Array
        • Alt-Splicing Analysis of Exon Array
      • NCBI GEO Importer
    • Webinars
    • White Papers
      • Allele Intensity Import
      • Allele-Specific Copy Number
      • Calculating Genotype Likelihoods
      • ChIP-Seq Peak Detection
      • Detect Regions of Significance
      • Genomic Segmentation
      • Loss of Heterozygosity Analysis
      • Motif Discovery Methods
      • Partek Genomics Suite Security
      • Reads in RNA-Seq
      • RNA-Seq Methods
      • Unpaired Copy Number Estimation
    • Release Notes
    • Version Updates
    • TeamViewer Instructions
  • Getting Help
    • TeamViewer Instructions
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On this page
  • Data Viewer
  • Terminology
  • FAQs
  • How do I get started and navigate the data viewer?
  • How do I make a plot?
  • Can you have multiple plots on the sheet?
  • When there are multiple plots, how are they controlled and configured?
  • My screen is full of plots. How do I add more plots without starting a new data viewer session?
  • Why does some data highlight in green when I hover over it?
  • How do I color my plot by a gene?
  • Can I plot genes from tables without going back to the analysis pipeline?
  • How do I manipulate my plot without using Tools or Configure?
  • Setup
  • New plot
  • Get Data
  • Tools
  • Select & Filter
  • Classify
  • Additional actions
  • Configure
  • Description
  • Axes
  • Content
  • Style
  • Grouping
  • Statistics
  • Background
  • Control
  • Heatmap & Bubble map
  • Additional Assistance
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  1. Partek Flow
  2. User Manual

Data Viewer

PreviousFeature linkage analysisNextVisualizations

Last updated 4 months ago

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.

  • If multiple plot types are selected together with ctrl-click or shift-click, only the plot configuration controls that are shared will be available for use.

  • 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:

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?

  • 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

  • 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.

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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). For example, 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

Additional Assistance

Node - data results from the analysis pipeline

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.

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.

Common controls: Save - overwrite a saved session Save as - save a new session using a new name Undo - recover backward actions

Redo - recover forward actions Export image - download one plot of all plots in a view to your computer

Send to notebook - save an image of the entire sheet (all of the plots in view) to the notebook Capture video - Start capturing a video of the sheet with various formats (nice for 3D scatter plots)

Setup: New plot - icons used to make a new plot

Get data - select data from the analysis pipeline

Tools: Select & filter - make selections and filter Classify - modify and apply selections as classifications Additional actions - create a feature list

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.

Selection (in the left-side menu for setting manual or criteria selections and on the right side of individual plots for manual selection by Pointer mode (click to select points), Rectangle mode (draw rectangle to select points), Ellipse mode (draw ellipse to select points), or Lasso mode (draw lasso to select points) 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 with Export image and Send to notebook or independently within each plot with Export image and Send to notebook.

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.

Select & Filter - applies to all of the plots on the sheet.

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

Sheet navigation uses a panel at the bottom of the screen . Use to Add a sheet or the to Duplicate, Rename, or Delete a sheet.

Any data highlighted in a green background when hovered over can be dragged and dropped onto a blue target .

Drag and drop manipulation is also possible for data nodes present in the configure icons (e.g., Axes and Style).

Open the Style icon and change Color by. Make sure you are on the appropriate node . Some plot types (e.g., tSNE) will invoke Style by clicking the legend. This is where you would color by a feature list that you have saved under list management.

The tables can be plotted on the sheet. One way to do this is to choose New plot , select Table (only data in table format are available), then the data to plot. Features are now available to drag and 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.

New plot

Get Data

Select & Filter

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.

Manual governs in plot selections which can undergo filtering or classification.

Criteria allows additions according to the selected node (this is criteria used to configure the plot like attributes or genes).

When criteria are added, the icon will grow with the selections. Remove the selections by clicking .

to include selected points

to exclude selected points

to remove filters

Classify

Additional actions

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.

Description

Axes

Features and attributes can be dragged to the Axes card . Alternatively, drag feature and attributes from the axis to plots using the data node .

Content

Style

Grouping

Statistics

Background

Control

Please see for details related to configuring a heatmap or bubble map in the data viewer.

If you need additional assistance, please visit to submit a help ticket or find phone numbers for regional support.

Hierarchical Clustering Configuration Settings
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Classify
Additional actions
Configure
Description
Axes
Content
Style
Grouping
Statistics
Background
Control
Heatmap & Bubble map