NEWS

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spatialHeatmap 2.11.2 (2024-07-23)

• The function cvt_id accepts vectors.

spatialHeatmap 2.11.1 (2024-06-14)

• Fixed some contrasts in spatial enrichment.

spatialHeatmap 2.9.6 (2024-04-16)

• The option of pairwise comparision is added in spatial enrichment.
• The layout of static network graph is improved.

spatialHeatmap 2.9.4 (2024-02-10)

• Added the formal citation.

spatialHeatmap 2.5.4 (2023-04-14)

• Developed the SPHM class for storing aSVG, bulk data, single-cell data, and matching list.
• Spatial Enrichement: outlier spatial featuers in references are supported.
• Shiny App: added K-means clustering, functional enrichment, and cluster downloading, redesigned Data Mining and Spatial Enrichment.
• Updated data structures in the background (R functions, Shiny App), and data pre-processing steps in SHM.
• Co-visualization: developed a new feature of coloring each cell by its own value of a chosen biomolecule; developed a new feature of co-visualizing bulk and spatially resolved single-cell data; developed a new feature of visualizing deconvolution results.

spatialHeatmap 2.3.1 (2022-10-22)

• In co-visualization, a new feature of bulk-to-cell mapping was developed, co-clustering method was simplified, and Shiny app was updated with options of Annotation/manual, Automatic, cell2bulk, bulk2cell.
• An S4 class of "SVG" was developed to store aSVG instances.
• Vignettes were updated.

spatialHeatmap 2.1.1 (2022-04-06)

• Developed the new functionality co-visualization of bulk and single cell data through auto-matching/coclustering, i.e. source bulk tissues are matched/assigned to single cells automatically through coclustering. This feature is implemented in both command line and Shiny app with testing data provided.
• Developed optimization functions for coclustering workflow with testing data provided.
• Co-visualization through manual matching was implemented in command line.

spatialHeatmap 1.99.0 (2021-10-14)

• Implemented overlaying feature: overlay template images in raster format with SHMs, where charcoal and transparency options are provided.
• Implemented Spatial Single Cell functionality: co-visualize single cells and bulk tissues by placing single-cell embedding plots (PCA, tSNE, UMAP) and SHMs side by side, cell cluster assignments are defined in the app or provided by users, in dimensionality plots shapes are not restricted to 6, etc.
• Spatial enrichment was synced to R command line.
• Implemented Sigle and Multiple search mode for gene IDs.

spatialHeatmap 1.1.6 (2021-05-17)

• The spatial heatmaps are able to maitain outline (stroke) widths defined in aSVG. The stroke widths can be updated with "update_feature".
• Text in aSVGs can be independent from features, i.e. have separate colors, stroke widths, etc.
• Only "g", "path", "rect", "ellipse", "use", and "title" elements are allowed in aSVG files, and other elements will raise errors or warnings. The "use" element should not in "g", and "g" elements should not have the "transform" attribute with a "matrix" value.
• Extraction of shape coordinates includes two alternative methods. If one fails, the other will be used by default. So in most cases though some coordinates are missing due to irregular shapes, spatial heatmaps can still be created.
• Added spatiotemporal example of rice coleoptile to Shiny app and vignette.
• Downloaded gene expression data are cached.
• In "spatial_hm", the "tis.trans" argument was replaced by "ft.trans"; width and height arguments were removed, since the spatial heatmap aspect ratio is set the same with original aSVG.
• Shiny app: the function "shiny_all" was renamed to "shiny_shm"; the app is able to take HDF5 database backend, which contains data and aSVG files, and the HDF5 database can also be uploaded on the user interface; re-organized user interface: Landing Page (includes links to different app instances), Spatial Heatmap (includes sub-tabs of Image, Interactive, Video, Matrix Heatmap, Interactive Network), Spatial Enrichment (identifies spatial feature-specific genes), About; new functionality introduced: auto-completion search box, URLs of specific app states can be bookmarked, full screen, scrolling height, tooltip, one-to-multiple re-matching of spatial features, fixed aspect ratio (SHMs are not squeezed in the case of multiple aSVGs), metadata column and link column in the data matrix; code was organized in modules, etc.

spatialHeatmap 0.99.0 (2020-09-21)

• Submitted the first version to Bioconductor.