Changelog
semla 1.2.0
2024-09-27
Bug fixes
Dealt with an issue in
MapFeatures
andMapLabels
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 inReadVisiumData
). - New arguments,
shape
andspot_side
, within theMapFeatures
,MapLabels
,MapFeaturesSummary
,MapLabelsSummary
, andMapMultipleFeatures
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 theUpdateSeuratFromSemla
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
whenstore_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"
inPlotFeatureLoadings
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 inAnglePlot
andMapFeaturesSummary
. - Changed example
Seurat
object to contain basic array coordinates.
Added
- Option to set
launch.browser
inFeatureViewer
. For instance, users can selaunch.browser = getOption("viewer")
inFeatureViewer
to launch the app in the RStudio viewer window. -
CreateStaffliObject
now accepts basic array coordinates to be stored inmeta_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 1.1.4
2023-09-04
Bug fixes
- Fixed bug in
LoadScaleFactors
- Fixed bug in
FeatureViewer
when handling data sets with spots located outside the H&E image
Added
- Added support for conversion of
Seurat
objects with Slide-seq data inUpdateSeuratForSemla
- Added option to color background and titles in
ImagePlot
- Added support for Visium + IF data in
LoadAndMergeMatrices
andReadVisiumData
- Added
renv.lock
file for installing semla and its dependencies withrenv
semla 1.1.0
2023-08-14
Added
- Added helper function for
Staffli
objects:-
GetScaleFactors
to fetchtibble
with scale factor related information
-
-
GetImages
to fetch images -
GetImageInfo
to fetchtibble
with image related information -
ReplaceImagePaths
to validate and update image paths - Added
UpdateSeuratForSemla
to makeSeurat
objects with VisiumV1 data compatible withsemla
- Added
LoadAnnotationCSV
to load annotations exported from Loupe Browser
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
andReplaceImagePaths
) - 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:
- Interactive data visualization and annotation with the
FeatureViewer
web app - Spatially aware analysis methods:
RegionNeighbors
,RadialDistance
,CorSpatialFeatures
,RunLocalG
,RunLabelAssortativityTest
,RunNeighborhoodEnrichmentTest
,CutSpatialNetwork
- Visualization methods:
MapFeatures
,MapLabels
- Image processing:
MaskImages
,RigidTransformImages
,RunAlignment
- Cell type mapping:
RunNNLS
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