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Changelog

semla 1.3.1

2025-03-19

Changes

  • If the spot barcode IDs are missing a “-N” (e.g. “-1”) suffix (like is standard in Visium data), it will be added to the IDs when running ReadVisiumData(). This ensures that multiple samples can be added and merged properly without conflicts with unique barcode identities.

  • Minor edits to the backend code for plotting functions

semla 1.3.0

2025-02-26

Added

  • Functionalities added for creating a spatial multimodal object using the new function CreateMultiModalObject(). This new function takes two objects, which have had their pixel coordinates aligned to each other beforehand, and joins them into a new object where the spatial points from the second “mapping” modality are mapped and aggregated onto the first “reference” modality. The data in the two modalities are stored as separate assays in the new object.

Changes

  • Changed the appearance of the color scalebar in MapFeatures() and MapMultipleFeatures() so that the ticks and outline colors are black and have the same linewidth.
  • MapFeaturesSummary() now has a default option set for the subplot_type argument (dafault = “violin”).

Bug fixes

  • Minor fixes in function documentations

semla 1.2.1

2025-01-24

Bug fixes

  • Fixed an issue with the RadialDistance() function to make it possible to pass additional arguments, such as maxDist and nNeighbors. Related to Issue #36

Added

semla 1.2.0

2024-09-27

Bug fixes

  • Dealt with an issue in MapFeatures() and MapLabels() if the specified column contains NA values and when using SeuratObject v.5.

  • When running RegionNeighbors() and specifying a column in which labels contain any blank spaces, the function will abort and a message will be provided. (#20)

Added

  • Compatibility with parquet file format, used in Visium HD, when loading coordinate files using the LoadSpatialCoordinates() function (used in ReadVisiumData()).
  • New arguments, shape and spot_side, within the MapFeatures(), MapLabels(), MapFeaturesSummary(), MapLabelsSummary(), and MapMultipleFeatures() functions to allow for square pixel plotting, particularly useful when working with Visium HD data.
  • A new vignette to demonstrate how to work with Visium HD data has also been added to the website.
  • Added a new argument, image_use, to the UpdateSeuratFromSemla() function, allowing the user to decide if they want to put the raw or the transformed image in the new object (#33).
  • Optional alternative to compute p-values when calculating spatial autocorrelation scores using CorSpatialFeatures(). The p-values are computed using the Student t Distribution, and adjusted p-values are calculated using the Benjamini & Hochberg (BH, or FDR) method. (#22)

semla 1.1.6

2023-09-19

Bug fixes

  • Fixed bug in RunLocalG when store_in_metadata = FALSE and no alternative hypothesis is provided.
  • Fixed bug in TileImage() when using multiple threads on linux.

Changes

  • Modified behaviour of mode = "heatmap" in PlotFeatureLoadings() to make sure that features are ordered by their highest dimensionality reduction value.
  • Updated NNMF vignette with a new data set.
  • Changed deprecated ggplot2 function arguments in AnglePlot and MapFeaturesSummary().
  • Changed example Seurat object to contain basic array coordinates.

Added

  • Option to set launch.browser in FeatureViewer(). For instance, users can se launch.browser = getOption("viewer") in FeatureViewer() to launch the app in the RStudio viewer window.
  • CreateStaffliObject() now accepts basic array coordinates to be stored in meta_data slot. These coordinates are defined on the capture array grid of a 10x Genomics Visium slide and do not match the H&E images.

semla 1.1.5

2023-09-06

Bug fixes

  • Added check for non-finite values when visualizing numeric data in FeatureViewer() to avoid crash
  • Fixed bug in FeatureViewer() when a slot other than ‘data’ is selected

semla 1.1.4

2023-09-04

Bug fixes

Changes

  • Improved function documentation

Added

Website

  • Updated image alignment vignette
  • Updated Staffli objects article
  • Added cell type deconvolution benchmark article
  • Added Visium + IF data vignette
  • Added example to digital unrolling vignette

semla 1.1.0

2023-08-14

Added

Changes

  • Improved verbosity
  • Reduced size of example data
  • Updated function documentation
  • Updated function examples
  • Added option to load images from URL instead of local path (LoadImages() and ReplaceImagePaths())
  • Added option to use multiple cores for ExportDataForViewer()
  • Fixed bug in RadialDistance() when no spots are available after removing singletons
  • Fixed bug in MergeSTData() when merging two or more objects containing multiple tissue sections
  • Fixed bug in MapMultipleFeatures() when NA values are present
  • Updated data loaders for increased compatibility with CytAssist data. Minor bug fixes for edge cases when spots are located outside of the H&E image
  • Fixed bug in LoadAndMergeMatrices() when loading data from a data folder output by Space Ranger
  • Changed output of AdjustTissueCoordinates() which now returns unadjusted y-axis values

semla 1.0.0

2023-03-24

We are excited to announce the first release of our R package, semla.

The package is designed to process, analyze and visualize Spatially Resolved Transcriptomics (SRT) data.

Key features of this release include:

We would like to express our gratitude to Javier Morlanes and Marcos Machado who contributed to this release. We appreciate your feedback, suggestions, and bug reports.

We invite users to download and install the development version of the package from our GitHub repo and explore the features and functionality. Please feel free to provide feedback and suggestions for future improvements.

Thank you for your support and we look forward to continuing to enhance and improve this package.

Sincerely,

Ludvig Larsson and Lovisa Franzén