New Features in the NG-CHM Viewer and Builder

ngchm viewing

Version 2.20.0 of the Next-Generation Clustered Heat Map (NG-CHM) viewer is now available. Significant new features in recent versions are listed below:

Version 2.20.0

  • Allow user to create multiple detail (zoomed) panels. Can be used to view widely-separated parts of a large NG-CHM side-by-side.
  • Add “Full-Screen” button to the top left of all panels. When pressed, the panel expands to occupy (temporarily) the entire panel area, hiding the other panels. Pressing the button a second time shrinks the panel to its original size and redisplays the other panels.
  • Implement a much improved system for adding embedded NG-CHMs to HTML pages.
  • Add support for plugins to query the NG-CHM for property values. This is used by the PathwayMapper tool to retrieve NDEx UUIDs included in an NG-CHM under the “ndexUUIDs” property. If any UUIDs are found, a menu entry for loading those pathways is created.
  • Enable the species identifier used by linkouts that are species specific to be specified by the NGCHM “bio.species” property (defaults to “Homo_sapiens”).
  • Add new default linkouts to the Cancer Dependency Map and GTEx.
  • Fix issues with the preferences panel.
  • Fix numerous miscellaneous bugs.

Version 2.18.3

  • Add default linkouts and standard type names for metabolites. New metabolite-related linkout targets include the Metabolomics Workbench, HMDB, PubChem, KEGG, ChEBI, and MetaCyc.
  • Add “-HTML” switch to shaidyMapGen to enable output of a standalone HTML file containing the NGCHM.

Version 2.18.2

  • Generate more-secure, random nonces for authenticating plugins to the NG-CHM viewer.
  • Fix miscellaneous bugs.

Version 2.18.1

  • Use missing color instead of black for missing values.

Version 2.18.0

Most of the changes in this release affect the NG-CHM Viewer.

The most obvious is a more flexible panel interface. Previously, the NG-CHM window was divided into two panels: a summary view on the left and a zoomed view on the right. You could change the relative proportions of the two panels but that was all. You can now create additional panels and change the panel(s) in which the summary and zoomed views are displayed. You can also choose to display some linkouts in a designated panel. (Some sites forbid being displayed in a panel.)

This video summarizes the new interface.

The new interface enables computational tools to interact with the NG-CHM. This video, starting at about 1:33, briefly shows two such tools. This video shows how the new features can be used in the analysis of single cell data.

In addition to many minor bug fixes, other notable changes in this release include:

  • Viewer: The detail panel zoom controls have moved to the panel header of the detail pane.
  • Viewer: A new menu before the search input lets you search within covariate bars instead of the labels.
  • Viewer: A new menu after the search input lets you search only the row axis labels, only the column axis labels, or both. This setting also affects navigation within the search results using the arrow buttons.
  • PDF Generator: Fix incorrect calculation of the number of missing values.
  • PDF Generator: Fixed issue whereby titles could overwrite legends.

Version 2.16.0

Most of the changes in this release affect the NG-CHM Builder. The most obvious are the improved user feedback during long clustering operations and the avoidance of duplicate computations when moving between pages.

Viewer:

The following changes affect the NG-CHM Viewer, including all the tools that embed the viewer (e.g. Builder, Galaxy, GenePattern):

  • Viewer: Allow tools that embed NG-CHMs to take over the display of covariate legend info.
  • Viewer: Update standard linkouts.
  • Viewer: Fix infinite loop when trying to determine the size of the summary NG-CHM on a small device.
  • Viewer: Fix bug in scatterplot covariate bounds that caused no covariates to be displayed.
  • Viewer: Fix handling of relative vs. absolute paths in CFG.api.
  • Viewer: Make covariate bar legends on PDF match those in the viewer.
  • Viewer: Fix sizing issue that caused the hamburger menu to be obscured.

Builder:

  • Builder: Add progress timer for long operations (such as clustering large matrices).
  • Builder: Generate data tiles only when needed instead of for every page.
  • Builder: Increase the maximum up-loadable matrix file size.
  • Builder: Ensure the builder version number is displayed in the About popup.
  • Builder: Fix incorrect truncation of column labels in “R formatted” matrix files (one less field on the header line).
  • Builder: Fix Transform screen losing track of the last transform change in the history list.
  • Builder: Do not start a new clustering process if the user reloads the page during clustering.
  • Builder: Improve checks for disallowed characters in covariate names.
  • Builder: Fix spinning wheel continuing to run following an error on the Matrix screen.
  • Builder: Remove redundant row and column size warnings for large matrices on the Transform screen.
  • Builder: Fix an issue whereby problems with filtering data can lock up the browser.
  • Builder: Fix incorrect parsing of numbers without a digit between the minus sign and decimal point on the Format Heat Map page.
  • Builder: Fix a race condition that allowed the user to bypass the matrix size limits.
  • Builder: Improve builder log messages.
  • Builder: Allow the user to add a covariate when no covariate file has been selected after one covariate has been uploaded.
  • Builder: Fix a bug that prevents user from changing the colors of Cluster-Based Covariate bars.
  • Builder: Fix a bug that used the wrong name or wrong colors for color palette for continuous color covariates.
  • Builder: Ensure that Bar and Color Types are compatible.
  • Builder: Fix issues related to the display of pages containing embedded NgChms in recent versions of Chrome.

Map Generator:

The following changes affect the Heatmap Data Generator, which is common to all of the various build platforms (Builder, R, Galaxy, GenePattern):

  • MapGenerator: Improve performance and reduce memory consumption.
  • MapGenerator: Add option to HeatmapDataGenerator for skipping tile generation.

Version 2.14.2

  • Fix bugs related to multiple embedded viewers on a page.

Version 2.14.1

  • Fix bug that prevented the stand alone and embedded viewers from opening old ngchms.

Version 2.14.0

  • The NG-CHM viewer page is now compliant with the HTML5 standard.
  • Many aspects of the UI are faster and smoother. In particular, ‘Flick view’ is now fast even on large maps.
  • The embedded viewer can be customized to send the details of map entries clicked on by the user to the enclosing web page.
  • The closure compiler instead of yui is used to generate the standalone viewer and the NGCHM widget.
  • Numerous other minor improvements and bug fixes.

Version 2.6.1

  • Improve top bar layout in Firefox.
  • Fix bug that prevented detail pop-up from being dismissed.

Version 2.6.0

  • You can now append a search string to the URL to the viewer; for example &search=GeneName. The map will open with any matching labels preselected.
  • All modal popups can now be moved by dragging the popup’s header bar.
  • The width of the summary panel is now an editable parameter in the Viewer preferences panel. You can still directly alter the summary panel width by dragging the vertical separator between the summary and detail panels.
  • The positioning and aesthetics of the Viewer’s “bubble help” have been improved.
  • In PDFs generated by the Java builder, row and column labels no longer include any hidden data fields, matching the behavior of the Viewer.
  • The Viewer’s help page has been refreshed.
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