Changes in version 1.7.7 BUG FIXES - Fixed a bug where the using the left-mouse click was not working for annotating individual spots under the "gene (interactive)" tab. Changes in version 1.7.6 NEW FEATURES - vis_gene_p(), vis_clus_p() and all related functions now have an argument point_size which lets you control how big the points are plotted. This can be useful for visualization purposes. - The shiny app now has an input controlling the point size. If you increase it to say 5, then if you zoom in the clusters (interactive) panel, you can see larger spots when zooming in. - These features are related to https://github.com/LieberInstitute/spatialLIBD/issues/28 although the spot diameter is still not the true spot diameter. However, now you have more flexibility for visualizing the spots. Changes in version 1.7.5 NEW FEATURES - Expanded the Using spatialLIBD with 10x Genomics public datasets vignette to show how you can deploy your web application. See https://libd.shinyapps.io/spatialLIBD_Human_Lymph_Node_10x/ for the live example. Changes in version 1.7.4 BUG FIXES - vis_gene() and vis_grid_gene() now support geneids that are found in the rownames(spe). This makese these functions more flexible. - vis_grid_gene() and vis_grid_clus() now have the sample_order argument which gives you more control in case you want to plot a subset of samples. This should also reduced the memory required as discovered at https://github.com/LieberInstitute/spatialDLPFC/issues/45. Changes in version 1.7.3 NEW FEATURES - Added support for more than one background picture per sample. This was done through the new argument image_id. Resolves https://github.com/LieberInstitute/spatialLIBD/issues/25. - Added options for side by side visualization of the background image and the clusters or gene expression values in the static versions. Resolves https://github.com/LieberInstitute/spatialLIBD/issues/19. - Allow changing the transparency level of the spots with the alpha argument. Resolves https://github.com/LieberInstitute/spatialLIBD/issues/20. - Add support for image manipulation with the magick package. Adds functions img_edit(), img_update() and img_update_all() as well as new features on the web application. Resolves https://github.com/LieberInstitute/spatialLIBD/issues/21. - Added support for more control over the gene color scale and in the web application also added support for reversing the order of the scale. Resolves https://github.com/LieberInstitute/spatialLIBD/issues/22 and https://github.com/LieberInstitute/spatialLIBD/issues/23. - Added export_cluster() and import_cluster() to help export/import clustering results instead of having to save large spe objects when exploring different clustering methods. - Added locate_images() and add_images() for adding non-standard images to a spe object. Changes in version 1.7.2 BUG FIXES - Fixed an issue introduced by newer versions of shiny. This version of spatialLIBD works with shiny version 1.7.1, though it's likely backwards compatible. Resolves https://github.com/LieberInstitute/spatialLIBD/issues/24. - Fix an issue where as.data.frame(colData(spe)) uses check.names = TRUE by default and then changes the column names unintentionally. Changes in version 1.7.1 NEW FEATURES - Added read10xVisiumWrapper() and related functions that make it easier to read in the SpaceRanger output files and launch a shiny web application using run_app(). These new functions read in the analysis output from SpaceRanger by 10x Genomics, in particular, the clustering and dimension reduction (projection) results. Changes in version 1.3.19 SIGNIFICANT USER-VISIBLE CHANGES - spatialLIBD has been updated to work with SpatialExperiment version 1.1.701 which will be released as part of Bioconductor 3.13. This changes internal code of spatialLIBD which will work with any objects created with SpatialExperiment version 1.1.700. Changes in version 1.3.16 SIGNIFICANT USER-VISIBLE CHANGES - The citation information has changed now that spatialLIBD has a bioRxiv pre-print at https://www.biorxiv.org/content/10.1101/2021.04.29.440149v1. Changes in version 1.3.15 SIGNIFICANT USER-VISIBLE CHANGES - We now use plotly::toWebGL() to make the web application more responsive. Changes in version 1.3.14 SIGNIFICANT USER-VISIBLE CHANGES - The documentation and help messages shown in the web application have been revamped and improved. Changes in version 1.3.12 NEW FEATURES - We added a new vignette that shows how you can use spatialLIBD with any 10x Genomics Visium dataset processed with spaceranger. The vignette uses the publicly available human lymph node example from the 10x Genomics website. Changes in version 1.3.3 NEW FEATURES - Overall the package has been updated to use SpatialExperiment version 1.1.427 available on Bioconductor 3.13 (bioc-devel). Several functions were re-named such as sce_image_gene_p() now has a shorter name vis_gene_p(). This update also changes these visualization functions to ONLY support SpatialExperiment objects instead of the original modified SingleCellExperiment objects. - Updated citation information to reflect that https://doi.org/10.1038/s41593-020-00787-0 is now public. Also added a link on the README to https://doi.org/10.6084/m9.figshare.13623902.v1 for the manuscript high resolution images. Changes in version 1.1.7 NEW FEATURES - The functions sce_image_gene_p(), sce_image_gene(), sce_image_grid(), sce_image_grid_gene(), sce_image_clus(), sce_image_clus_p(), geom_spatial() now work with VisiumExperiment objects thanks to the new function read_image() and ve_image_colData(). This work was done by Brenda Pardo and Leonardo. Changes in version 1.1.5 NEW FEATURES - fetch_data() takes the data from sce object and creates a VisiumExperiment object containing these data thanks to the function sce_to_ve(). VisiumExperiment object can be obtained with fetch_data("ve"). This work was done by Brenda Pardo and Leonardo. Changes in version 1.1.4 NEW FEATURES - fetch_data() now uses BiocFileCache() when downloading the data from Dropbox. Changes in version 0.99.14 SIGNIFICANT USER-VISIBLE CHANGES - Added the function enough_ram() which is used to control the execution of examples. If it fails when using fetch_data("sce") then fetch_data() will show a warning. - fetch_data(type = "sce_example") is now supported and used visibly in the vignette, eliminating the need for eval = FALSE chunks. This should enable testing the vignette code on the Bioconductor Single Package Builder on Windows (max 2.5 GB of RAM available). BUG FIXES - Fixed the example in get_colors(). - Fixed layer_stat_cor_plot() for when min and/or max are specified. Changes in version 0.99.13 SIGNIFICANT USER-VISIBLE CHANGES - Documentation website is now available at http://LieberInstitute.github.io/spatialLIBD/. It gets updated with every commit on the master branch (bioc-devel) using GitHub Actions and pkgdown. Changes in version 0.99.12 BUG FIXES - Remove the spatialLIBD.Rproj file =( since BioC's SBP is asking me to do so http://bioconductor.org/spb_reports/spatialLIBD_buildreport_20200303135350.html - Use system2() instead of system(). - Move the set.seed() call outside of layer_boxplot() as noted by Martin Morgan https://github.com/Bioconductor/Contributions/issues/1389#issuecomment-594099852 . - Use \linkS4class as I see being done at https://github.com/drisso/SingleCellExperiment/search?q=linkS4class&unscoped_q=linkS4class. - Use vapply() instead of sapply(). - Fix (or attempt to) some doc links. Changes in version 0.99.11 BUG FIXES - Check if removing the RcppAnnoy line in the DESCRIPTION actually works now based on Aaron Lun's comment at https://github.com/eddelbuettel/rcppannoy/issues/57#issuecomment-594097241. Changes in version 0.99.10 SIGNIFICANT USER-VISIBLE CHANGES - Include AWS links to the image TIFF files (~500mb each) as requested by Qian Zhu zqian@jimmy.harvard.edu for visualizing the data on the Giotto Viewer https://www.biorxiv.org/content/10.1101/701680v1. BUG FIXES - Fix fetch_data() and the vignette by specifying the mode = "wb" for utils::download.file() in order to resolve an issue with Windows OS reported here http://bioconductor.org/spb_reports/spatialLIBD_buildreport_20200302120158.html#tokay2_buildsrc_anchor. Changes in version 0.99.9 SIGNIFICANT USER-VISIBLE CHANGES - Link to https://doi.org/10.1101/2020.02.28.969931 now that its public. Changes in version 0.99.8 SIGNIFICANT USER-VISIBLE CHANGES - https://spatial.libd.org/spatialLIBD is not supported since we are using Shiny Server and not Shiny Server Pro. So all links have now been updated to http://spatial.libd.org/spatialLIBD. Changes in version 0.99.7 BUG FIXES - Run a test that might help with https://github.com/r-lib/pkgdown/issues/1230. Changes in version 0.99.6 SIGNIFICANT USER-VISIBLE CHANGES - Add mirrors for the shiny app and change the main location. Changes in version 0.99.5 SIGNIFICANT USER-VISIBLE CHANGES - Make fetch_data() more flexible. Should now work when the data is absent. Changes in version 0.99.4 BUG FIXES - Fix Travis badges - Fix Kristen's name on the vignette - Add the same welcome information to the top of the vignette, since this will be what Bioconductor users see first. Basically, we have made sure that users will see the same information first regardless if they find the package README, open the shiny app, or find the package vignette. Changes in version 0.99.3 SIGNIFICANT USER-VISIBLE CHANGES - Further refine the READMEs (pkg and shiny). They now include the list of links to the raw 10x Genomics files as well as a short description of the project at the top. This was in response to feedback by Andrew Jaffe. Changes in version 0.99.2 SIGNIFICANT USER-VISIBLE CHANGES - Update main package READMEs to reflect the changes to the shiny web app README.md. Changes in version 0.99.1 NEW FEATURES - Added Kristen R Maynard to the DESCRIPTION file. - Improved the shiny app page footer. - Moved around the documentation and added a new main tab with an overview in response to the feedback by Stephanie Hicks. Changes in version 0.99.0 NEW FEATURES - Added a NEWS.md file to track changes to the package. - First full version of the package to be submitted to Bioconductor. Note that the ExperimentHub::ExperimentHub() functionality won't work until they approve the package. However, for now fetch_data() has a backup mechanism in place. - Submitted to Bioconductor here.