1.6.0 Release Notes

Highlights

  • Mouse-Over Information shown for both cells and genes within Graph Windows. This means that researchers can now very quickly determine the identity of individual dots in their plots with ease. We’ve also added the ability to “pin” the parameter names in GeneView plots to graphs within the Layout Editor, so that these annotations become available for export and publication. 
  • High-Resolution Figures—up to 4096 x 4096 pixels—are now available. This will make your figures for publication pop in a way never before possible. In addition, the seed for contour plots is now adjustable in order to better illustrate populations of any size within that plot type. 
  • Dot Shapes can be adjusted within dot plots and dot plot overlays in the Layout Editor. Dot Sizes are also now editable on a layer by layer basis within the overlays. 
  • ParameterSets now available for filtering parameters within the Customize Axis scaling options associated with the Graph Window. 
  • Set a default geneset location in preferences, to have SeqGeq automatically add your favorite genesets to new workspaces. 

Fixes

  • For Mac installations only – The plugins folder is now included in the Demo Data folder again,  
  • New plugin, “Lex”, included in the installer automatically. Allows researchers to de-multiplex data automatically. Particularly useful if you’re workflow includes concatenating different datasets together – Lex can pull the concatenation apart, retaining sample names in the process. TopGenes and DEGenes (not recommended) were removed as default plugins from the installer. 
  • Additional demo data and geneset libraries added to installer by default. 
  • Support for latest HDF5 (“.h5”) file formats. 

Known Issues

  • Certain legacy workspace Layouts cannot be loaded into the latest release. Workaround: keep the older version of SeqGeq (v1.5) in order to access the previous work completed there, use the new edition to analyze new datasets.
  • Lex cannot de-multiplex populations combined directly from within a single sample. Workaround: Export subset populations as individual and properly named samples prior to concatenation.
  • Save button does not always create a proper analysis file, and this extends to the auto-save dialog created when closing a workspace. Workaround: Never use the “Save” option, nor-confirm a request to save when closing – Instead always use the “Save As” function. Also, we recommend saving revisions of the workspace in order to minimize the harm in case a workspace saves incorrectly. 
  • Overlays are not supported for GeneView in the Layout Editor. Workaround: “Fake the overlay” by aligning plots of interest horizontally an vertically, with the topmost plot’s background set to clear. Make sure to place the smaller of the two genesets on top.
  • Non-Unicode 8 characters (such as those in the Chinese alphabets) in a dataset’s file path will prevent data from being loaded into SeqGeq workspaces on Windows machines. Workaround: Make sure the file path leading to Gene Expression matrices are using only standard English character sets.
  • Heatmapping downsampled populations can lead to blank rows. Workaround: Downsample populations manually, as opposed to using the Downsampling platform when heatmapping downstream.
  • KMeans clustering does not perform an autogate to illustrate clusters as populations in the workspace. Workaround: Run the AutoGateCategorical plugin on the KMeans clustering parameter to identify those subpopulations.
  • Gating path names longer than about 30 characters cause errors in calculating p-Values in Gene View Workaround: Name populations judiciously.
  • Legacy workspaces with gates drawn in Gene View will need to be re-confirmed, as changes in this version may have altered their position or geometry.
  • “Export Eigen Vectors” button from Principal Component type Dimensionality Reduction dialog for Windows will default to save the vectors in a temporary forlder. Workaround: Make sure to save vectors to a common location, such as Desktop.
  • Bring forward command in Layout Editor gives bug reporting window. Workaround: Close the bug report window and continue analysis.
  • Derived Observations (e.g. PCA vectors) calculated for certain Derived Parameters (e.g. a Gene Set in Cell View) will not be correctly applied when re-opening a saved analyses. Workaround: Don’t apply Derived Observations to Derived Parameters.
  • Only demo data can be loaded when running SeqGeq in demo mode; i.e. concatenated data (even from demo files) cannot be loaded into SeqGeq in demo mode.
  • Some hotkeys meant to open tabs in the Workspace will generate a bug report window.
  • Bug reporting window does not send information to FlowJo, LLC. Workaround: Send an email to tech support for a speedy reply and troubleshooting: seqgeq@flowjo.com
  • The 24 hour authentication grace period for temporary offline access will sometimes fail to correctly activate.
  • Running tSNE on a raw expression matrix is not advised. Workaround: We recommend running tSNE on principal components, after running PCA on the expression matrix of interest.
  • On a Mac, R-based plugins fail to calculate if the file paths contains a space or other special characters. Workaround: Remove spaces and special characters from file paths associated with the analysis.
  • Parameter Selector for plugins won’t discriminate between identical samples opened in different workspaces (and uses the first workspace only). Workaround: Don’t open the same dataset in different workspaces simultaneously while attempting to access plugins.