Changelog

SpatialMap 0.20.0

• Fix an issue where updating dependencies introduced changes to clustering results, leading to failed builds.
• Dependencies have been updated to reflect new expectations.

SpatialMap 0.19.2

• Patch for uploadCellMetadata so that both cell_type_annotation_id and quality_filter_id arguments are persisted for neighborhood annotations.

SpatialMap 0.19.1

• patch for addCellMetadata–cell.ids passed as rownames or vector names will now appropriately map to cells in a SpatialMap object

SpatialMap 0.19.0

• pairwiseAdjacency will no longer return redundant interaction results when working with a symmetric NN
  • Previously, for any NN was specified, pairwiseAdjacency would return results for both A -> B and B -> A.
  • If the NN was symmetric, the results in both directions would be identical (the interaction is the same regardless of the directionality due to the symmetry).
  • This would return confusing “duplicate” results and also hurt the multiple hypothesis correction (within both pairwiseAdjacency and compareAdjacency)
  • This change is potentially breaking for old analyses since only one of the two directionalities will be returned, and more results will remain significant after multiple hypothesis correction is performed.
  • (semver says breaking changes don’t necessarily get a major version bump until 1.0.0)

SpatialMap 0.18.1

• Update broken links to Enable website

SpatialMap 0.18.0

• Adding unit tests for NN class validation
• A few bugfixes for validation code
• New functionality for validation–only non-zero positive integers accepted in idx slot. This would cause problems down the line before, catching it earlier will help reduce confusion as to the root cause.

SpatialMap 0.17.0

• Add a dist_filter option to the KNN and Delaunay graph computation options. This allows the user to exclude interactions beyond a certain distance, which may help ensure interactions represent genuinely plausible biological interactions.

SpatialMap 0.16.0

• Use interp package for Delaunay triangulation method of defining nearest neighbors
  • Add unit tests for this method
• A few cleanups for documentation of nearest neighbor graph functions

SpatialMap 0.15.0

• Add new function plotChordDiagram(), which allows visualization of cell-cell interactions from pairwiseAdjacency
  • Also allows for cohort grouping, producing grouped chord diagrams
• Add an error message to compareAdjacency that appears when no t-tests could be run due to insufficient sample size

SpatialMap 0.14.2

• Fix a bug where compareAdjacency would fail when run following pairwiseAdjacency using the permutation method.

SpatialMap 0.14.1

• Fix a bug where spatialmap_from_db would create duplicate study_id columns in projectMetadata
• Fix a bug where mergeProjectMetadata would not overwrite some existing columns even when overwrite = TRUE
  • Introduced a parameter update_already_merged_columns to control this behavior
• Fixes for updateProjectMetadata:
  • Ensure that any modified columns are properly updated in cellMetadata when expand_metadata = TRUE
  • When overwrite = FALSE, modified columns will be added and named "{original_colname}_upd"
• Fix a bug where removeCellMetadata would error when called
  • Also remove all parameter, which has been deprecated for a while
  • Also add a test for this function
• Clean up internal data frame subsetting (set drop = FALSE)
• Clean up temporary image download folder at the end of plotting vignette

SpatialMap 0.14.0

• New function updateProjectMetadata():
  • Updates the projectMetadata slot in a SpatialMap object such that they are up-to-date with the Enable Portal
  • Helpful to update metadata like region display labels, visual quality, and clinical metadata without requiring the user to rerun spatialmap_from_db.

SpatialMap 0.13.0

• Cleaning up some more package documentation
  • Added Examples (or Details pointing to specific vignettes) and Value sections to many functions.
  • Fixed a few typos
  • Some vignette cleanups & clarifications
• A few misc updates to vignettes
  • No longer include code running con <- emconnect() (cleanup from SDA migration)
  • Incorporate new facil::check_dir to facilitate running vignettes on Code Ocean
  • Letting plotImage demos run in plotting vignette (seems like previous CI issues have been resolved?)

SpatialMap 0.12.1

• Fixed bug in combineMaps where if object.list had names, combineMaps would throw an error.
  • Error was due to a mismatch between expected region names based on project metadata (rownames(projectMetadata(sm))) and spatialmap region object names (names(regions(sm))).

SpatialMap 0.12.0

• Added an error to pairwiseAdjacency calculations that will stop a user if their chosen feature has missing values, since these will cause most of the resulting stats to have NA values.
• Also, since factor levels are made extensive use of in the pairwiseAdjacency calculations, decided to drop factor levels from the feature to ensure that the only levels used are ones that are actually present in the data.

SpatialMap 0.11.0

• Added some functionality to .smapply that will warn users when the version of SpatialMap used to create the SpatialMap object they’re currently working on (or the version it was last repaired to) do not match the currently running version of the package.
  • While this isn’t foolproof, many/most operations on SpatialMap objects run through .smapply at some point, so this can provide some helpful guidance
  • The warning is set to print only once per session, but this behavior can be overridden by setting the env var “ALWAYS_WARN_VERSION” to “True”
  • Added an associated testing suite for the new functionality

SpatialMap 0.10.0

• Some cleanups to the documentation for Normalize and its associated helper functions.
  • Mostly fixing some typos and adding additional details
• Finally fully deprecating the batch correction functionality–underperformed in testing and was mostly unused. Functions still exist, but are no longer exported from the namespace.

SpatialMap 0.9.4

• Cleaning up some package documentation.
  • Added Examples (or Details pointing to specific vignettes) and Value sections to many functions.
  • Fixed a few typos
  • Some vignette cleanups & clarifications

SpatialMap 0.9.3

• Small improvement to FilterCodex: raise error when user hasn’t run QCMetrics first

SpatialMap 0.9.2

• Fix a bug where a pipe operator was missing in the Analysis Guide 3 vignette (appendix)

SpatialMap 0.9.1

• Fix a bug where plotImage functions sometimes fail when a scalebar value above 0 is provided

SpatialMap 0.9.0

• Added sample-level aggregation capability for pairwiseAdjacency and related functions
  • Now you can specify analyze = "sample_label" or any other grouping present in your object’s projectMetadata and pairwiseAdjacency will use the groupings specified in that variable to aggregate pairwise cell interaction counting and analysis across all Regions belonging to each sample.
  • Updates to compareAdjacency to handle the outputs of sample-level aggregation
  • Updates to plotPairwiseAdjacency to handle the outputs of sample-level aggregation (requires the same analyze parameter used by pairwiseAdjacency)
• Added a new feature to plotPairwiseAdjacency–now each plot will include the region ID or sample label in the plot’s title.
• Updates to vignettes and documentation explaining these new features.

SpatialMap 0.8.0

• New arguments (custom.qc.*) for FilterCodex allow for the specification of custom QC filters based on columns in cellMetadata
  • Added additional tests for this new functionality

SpatialMap 0.7.0

• Bug fix for .smapply and associated helper functions
  • Previously, if you created region-level NNs or Representations, then ran .smapply on an informal or formal analysis (e.g. "combined") the region-level NNs and Representations would be deleted. This bug ensures that those NNs and Representations persist.
• This bug fix required a few changes to generics (hence 0.7.0)
  • Change in the generic for Representations("Analysis", "missing") where it will always return a list instead of returning a Representation when only a single Representation exists
  • In addition, the generic for Representations("SpatialMap", "missing") will now print the analysis used, if any (should help with debugging)
  • Finally, the generic for NNs("SpatialMap", "missing") will now always return a list instead of returning an NN when only a single NN exists

SpatialMap 0.6.8

• Bumped emconnect to 1.23.2 in Imports

SpatialMap 0.6.7

• Remove check for valid connection in spatialmap_from_db, as this is handled by emconnect::translate_inputs

SpatialMap 0.6.6

• Fix an integer overflow issue that could occur when pairwiseAdjacency was run on larger regions
• pairwiseAdjacency now also computes and returns "log10.padj"
• plotPairwiseAdjacency now accepts "p.value", "p.adj", and "log10.padj" values for what

SpatialMap 0.6.5

• .smapply when using cat.output = "none" on an informal analysis now returns a list with items named by the groups in the analysis

SpatialMap 0.6.4

• Cleaning up some package documentation.
• Added Examples (or Details pointing to specific vignettes) and Value sections to many functions.
• Added a new argument to QCMetrics that was already present in the lower level qc_metrics, which allows the user to specify how repeated DNA channels in an image are handled.

SpatialMap 0.6.3

• Fixed bug in plotQCSummary caused by superfluous code

SpatialMap 0.6.2

• A few patches in preparation for flexible studies rollout (i.e., the ability to associate regions with multiple studies):
  • plotImage* functions resolve duplicate regions under the hood
  • Updates to unit tests for spatialmap_from_db and plotImage* to catch duplicate regions
  • Updates to Analysis Guide vignettes using these functions
• Bumped emconnect to 1.51.1 in Imports

SpatialMap 0.6.1

• Improved error messaging when a function cannot find the specified features within a Region object
• Bumped facil to 0.3.1 in Imports

SpatialMap 0.6.0

• Custom filenames can now be specified for export* functions using the file_names argument
  • Tutorial on Exporting Data is updated to provide examples of this
• Fix a bug in .smapply where Analysis names were not returned
• Fix a bug in compareAdjacency where grouping by a metadata column would error
• Clearer documentation for compareAdjacency and pairwiseAdjacency
• Changes to tests:
  • Clean up pairwise adjacency tests
  • Export test files are self-cleaned upon completion
  • Updated zarr test fixture for conversion from emObjects
• Remove RDS fixtures (now generated in CI)

SpatialMap 0.5.56

• Patching a bug in spatialmap_from_db where study_ids were not passed to emconnect::get_study_metadata. This would cause failures when building SpatialMap objects containing regions that belong to more than one study.

SpatialMap 0.5.55

• Patching a bug in addSelfInteractions where the index for the self interaction was taken from the cell_id rather than the position in the idx/dist slots. This would cause unexpected behavior when the object has been subsetted, or when the integer at the end of the cell names didn’t start at 1.

SpatialMap 0.5.54

• A few fixes in vignette formatting and content

SpatialMap 0.5.53

• Patch issue where uploadCellMetadata would fail when metadata_names was missing for some of the Regions

SpatialMap 0.5.52

• Patch issue where spatialmap_from_emobject failed when neutral.markers was specified but none were found

SpatialMap 0.5.51

• New function spatialmap_from_emobject allows users to convert emObjects stored on disk into SpatialMap objects
  • Note: this is currently only for internal users, but support for external users is on our roadmap!

SpatialMap 0.5.50

• Relax version requirement for ggplot2 import
• Bump version requirement for emconnect import

SpatialMap 0.5.49

• Patch issue where mergeProjectMetadata failed when projectMetadata has only one column

SpatialMap 0.5.48

• Patch issue where custom normalization returned an error when MARGIN = 2
• Allow user to specify whether to scale data before performing PCA

SpatialMap 0.5.47

• Improvements to smSubset:
  • Now accepts a remove argument, allowing users to specify which data to exclude when subsetting
  • Better error catching for case when all cells/Regions are removed
• Patch a broken reference link in Analysis Guide 7

SpatialMap 0.5.46

• plotRepresentation now allows users to subsample cells to a specified proportion

SpatialMap 0.5.45

• neighborhoodHeatmap now allows user-specifed clustering and dendrogram settings to override default values

SpatialMap 0.5.44

• New function addRepresentation allows users to easily add new representations to SpatialMap and Region objects

SpatialMap 0.5.43

• Minor change to filtering functions under the hood for compatibility with dplyr 1.0.10
• Key changes to renv.lock:
  • dplyr 1.0.10
  • tidyr 1.2.1
• Temporarily stop evaluating plotImage code chunks in the plotting tutorial vignette to unblock CI

SpatialMap 0.5.42

• Pin ggplot2 to version 3.3.6

SpatialMap 0.5.42

• Docs webpage updates

SpatialMap 0.5.41

• Added coverage reports via covr

SpatialMap 0.5.40

• Fixed bug in plotExpressionHeatmap that threw an error for single marker plots

SpatialMap 0.5.39

• Update Tutorial vignette on plotting to show all prior plotImage examples

SpatialMap 0.5.38

• Bump emconnect version (1.6.1) in lockfile
• Changes to support Zarr migration, which should not affect end users of plotImage*:
  • Update unit tests
• Minor update to Tutorial vignette on plotting

SpatialMap 0.5.37

• Fixed Analysis Guide 6 to show heatmaps

SpatialMap 0.5.36

• Added an intermediate check for regions that match given versions in spatialmap_from_db

SpatialMap 0.5.35

• Added a new set of padding arguments to plotting functions that return ComplexHeatmap objects.
  • ComplexHeatmap can have some trouble dealing with longer text labels, resulting in text getting cut off
  • New padding arguments allow users to add space to the edges of their plots, showing full text
  • Updated functions include plotExpressionHeatmap, plotPairwiseAdjacency, and neighborhoodHeatmap.
  • Default values for plotExpressionHeatmap have been modified such that the default legend is no longer cut off
  • Internal helper function padHeatmap is also exported from the namespace to facilitate modifications to already created heatmap objects
• Vignettes where these functions are used have been updated to make use of these padding arguments

SpatialMap 0.5.34

• Footer updated to include links to T&C, PP, and DLA

SpatialMap 0.5.33

• Correction to the vignette changes done in version 0.5.29 so they can pass the docker build.

SpatialMap 0.5.32

• Bump emconnect version (1.5.18) in lockfile
• Add link from Analysis Guide 5 to Advanced Spatial Tutorial

SpatialMap 0.5.31

• Patching bug in spatialmap_from_db where ds wasn’t being passed to emconnect::determine_data_versions

SpatialMap 0.5.30

• Bump emconnect version (1.5.17) in lockfile
• Changes to spatialmap_from_db:
  • New parameter markers allows specification of which biomarker data to pull
  • annotation_types now accepts “all” and “none” values

SpatialMap 0.5.29

• A few changes to vignettes (Analysis Guide 1 and plotting vignette) that will make them easier for users to run themselves

SpatialMap 0.5.28

• feature_vector is now deprecated in cellNeighborhoods. Users should add their feature using addCellMetadata and supply it to feature instead.

SpatialMap 0.5.27

• prevent failure in pairwiseAdjacency when a cell has zero neighbors
• check for pairwiseAdjacency result in compareAdjacency

SpatialMap 0.5.26

• Added a new Tutorial vignette, outlining all of the plotting functions in the package
• A few small cleanups to the documentation

SpatialMap 0.5.25

• Patched uploadCellMetadata. Now expects numerical instead of numeric as the data_type for numeric data in R to match the labels used for this type of data on the Portal.

SpatialMap 0.5.24

• Append unique index to each region’s spatial cluster during spatial QC to allow filtering on partition

SpatialMap 0.5.23

• move p-value adjustment from plotPairwiseAdjacency to pairwiseAdjacency
• save adjusted p-values back to SpatialMap object
• add trim and cuts (passed to facil::cleanMatrix) to plotPairwiseAdjacency
• some documentation cleanup

SpatialMap 0.5.22

• Add the function addProjectMetadata to enable updates to region-level metadata
• addCellMetadata now indexes by cell names if named metadata are passed
  • Added associated unit tests
• Minor updates to documentation for addCellMetadata

SpatialMap 0.5.21

• Fix a bug in neighborhoodClusters to ensure that neighborhoods are produced correctly when a SpatialMap object is passed

SpatialMap 0.5.20

• Allow filtering on max_dist.n for spatial QC
• Improve efficiency of filter_helper by using dplyr
• Clean up remaining tidy evals

SpatialMap 0.5.19

• Minor update to naming of “HLA-DR” in Analysis Guide 4 vignette
• Update lockfile
• Deprecate bucket parameter in plotImage calls as tiles are now pulled using Portal credentials instead of directly from S3
• Fix typing bug in getCellInteractions

SpatialMap 0.5.18

• Patched spatialmap_from_db’s call to get_cell_annotations (ensure length of versions matches length of acquisition_ids)

SpatialMap 0.5.17

• Patched spatialmap_from_db so that it correctly handles the case when no cell annotations are found
• Patched createRegionObject so that it correctly handles NULL being passed to cellMetadata

SpatialMap 0.5.16

Added

• A number of unit tests

Removed

• Cleaned up deprecated QC functions (related to expression_quantiles)

Fixed

• A bug in flexible_region_subset (a function that subsets Regions by XY coordinate)
• Minor cleanup to message printing & generics

SpatialMap 0.5.15

• Incorporated big emconnect update impacting the functionality of spatialmap_from_db
  • QC annotations generated on the Portal (or pushed from Workbench) will now be pulled in as annotation sets to the cellMetadata slot
  • Updated analysis guide 2 appendix instructions on how to work with QC filters generated on the portal
  • spatialmap_from_db now supports new arguments to emconnect::get_cell_annotations, annotation_ids, annotation_types, and vector_val_defaults

SpatialMap 0.5.14

• Consistently handle plot.titles.from for plotFilteredCells, regardless of object type (SpatialMap or Region) passed
• Add the same functionality for plotRepresentation
• Add unit tests for this functionality
• Deprecate use of ggplot2::aes_string
• Fix print bug in getActiveAnalysis, add unit tests for this

SpatialMap 0.5.13

• Allow specification of qc.var (column in cellMetadata holding QC results) in FilterCodex, and the following QC-related plotting functions: plotFilteredCells, plotFilterSummary, plotQCSummary
• Add unit tests for this functionality

SpatialMap 0.5.12

• Updates to vignettes
  • Analysis Guide 1 now includes more in-depth explanation of the neutral.markers parameter in spatialmap_from_db
  • Analysis Guide 2 now uses patchwork to make the plot visualization a bit cleaner
  • Analysis Guide 3 now links to guidance in the platform User Manual with best practices on unsupervised clustering
  • Intermediate .RDS fixtures are now tracked with git-lfs, and will be pushed to users’ spatialmap_vignettes folders
• Normalize now accepts "zscale" passed to method, matching recommendation in documentation
• spatialmap_from_db now looks in the global environment for con, matching emconnect convention for connections
• A few small fixes to the website
  • Copyright date
  • Linking to user manual for Workbench guidance and YouTube for video tutorials
  • Better narration on vignette homepage

SpatialMap 0.5.11

• Fixed issue with passing single segmentation & expression versions to uploadCellMetadata. Now back-compatible with older Portal tools.
• Add dry_run parameter to uploadCellMetadata to facilitate debugging

SpatialMap 0.5.10

• Add resources to export SM data. Features:
  • Allow export of per-region CSVs for all cell data and Region level metadata
  • Allow export of per-region CSVs for different slots individually
  • Allow export of data CSVs across multiple regions (via analyze parameter or activeAnalysis)
  • Unit testing
  • Vignette
• Significant updates to Representations and embeddings generics, resolving inconsistent method dispatch.
  • related unit tests

SpatialMap 0.5.9

• Update renv.lock file to fix CI

SpatialMap 0.5.8

• Update renv.lock file to point to updated Enable repo structure

SpatialMap 0.5.7

• Improve aesthetics of plotImage* output:
  • Fix overlapping colored text in marker legend overlay
  • Add translucent background to marker legend to improve readability (ggplot output only)
  • Option to add a scale bar
• Refactor plotImage.Region to wrap around plotImage.acquisition_id
• Tests for plotImage* functions
• CI only: split up devtools::test from devtools::check for clearer test results

SpatialMap 0.5.6

• Various changes related to image preparation/tiling updates in emconnect 1.4.10
• Update get_image to wrap around the emconnect function of the same name
• Rename plotImage.Region2 to plotImage.acquisition_id so that its function is clearer

SpatialMap 0.5.5

• Enforce consistent ordering of features in the Data method for SpatialMap objects

SpatialMap 0.5.4

• Streamline CI

SpatialMap 0.5.2

• During DB pull, do not pull data for acquisition_ids that lack version info.
• Fix an oversight in names()<- method for SpatialMap objects
• Fix a problem where not providing valid neutral.markers would cause an error
• Add validity check of neutral.markers and helpful related messages in DB pull

Add sameSM method, which checks that 2 Spatialmap objects are identical (helpful for testing!) Add inline testing for combineMaps

Unit tests for Utils-SM.R and one for IO.R Changes to internal toy datasets (skin, tonsil)

SpatialMap 0.5.1

• Added a few bits of polish to the vignettes & website
• Added README to vignette folder that will be pushed to users’ home directories
• Added a .json file to the vignette folder to define the hierarchy of folders in users’ home directories

SpatialMap 0.5.0

• First full release of Analysis Guide vignettes:
  • Revisions to analysis guides 5-6
  • Fully integrated all AG vignettes to work from CITN10 data pulled from ATLAS
  • Made some minor formatting changes to all AGs
  • Split off part of the previous AG5 into a tutorial vignette with a deeper dive on spatial analysis and graphs in SM

SpatialMap 0.4.85

• Patching [ generic to fix logical subsetting of regions

SpatialMap 0.4.84

• Update renv lockfile

SpatialMap 0.4.83

• Allow QCMetrics() to summarize across multiple DNA channels

SpatialMap 0.4.82

• Resolve errors in check() related to emconnect update
• Resolve documentation issues resulting from roxygen2 update

SpatialMap 0.4.81

** Updated spatialmap_from_db to reflect upcoming changes in emconnect.

SpatialMap 0.4.80

• Changes to the behavior of plotCellProportions, including:
  • Drop unused levels from the legend when select_var2 is specified
  • By default, compute and plot proportion of cells within var_sample (default: Regions) instead of counts
• Updates to documentation for compareCohorts and compareAdjacency
• Minor revisions to Analysis Guide vignette 7

SpatialMap 0.4.79

• Update to Analysis Guide vignette 7

SpatialMap 0.4.78

• Changed compareCohorts to make comparisons based on cell type proportions rather than cell type counts
• get_valid_metadata_counts is no longer an exported function

SpatialMap 0.4.77

• Fixed a bug in .smsubset where subsetting to an empty Region would break
• Changed the name to smSubset (old .smsubset will still work temporarily)

SpatialMap 0.4.75

• Changed the parameter select_cohorts to select_features for plotCohortsVolcano, to better align with the nomenclature used in compareCohorts

SpatialMap 0.4.74

• Bug fix in neighborhood calculations -problem handling missing factors
• progress = FALSE for simple smapply generics

SpatialMap 0.4.73

• Major pkgdown website updates including
  • CI workflow that auto-updates website
  • Standardization of pkgdown website building workflow
  • The ability to make automatic HTML website edits outside of pkgdown
  • The inclusion of the full User Journey

SpatialMap 0.4.72

• Fixed broken link in uploadCellMetadata documentation.

SpatialMap 0.4.71

• Update to analysis guide vignettes 1-4
• Changed file names of all vignettes to fit into new user journey framework

SpatialMap 0.4.70

• Fix duplicate checking for Region/Analysis validity check

SpatialMap 0.4.69

• Add color param to plotExpressionHeatmap

SpatialMap 0.4.68

• Quick bug fix for SummarizeFilters

SpatialMap 0.4.67

• Fix windowing bug in plotImage.Region2

SpatialMap 0.4.66

• SpatialMap package website updates

SpatialMap 0.4.65

• Added User Journey Analysis Guides 7 (Cohort comparison)

SpatialMap 0.4.64

• Small fix to plotCohortsVolcano to scale y-axis (p-value scale) to show 0

SpatialMap 0.4.63

• Added User Journey Analysis Guides 5 (Interactions) and 6 (Neighborhoods)

SpatialMap 0.4.62

• You can pass plot names (a metadata column) to plotFilteredCells

SpatialMap 0.4.61

Further refining the division of labor between emconnect and SpatialMap: * plotImage.Region now calls emconnect::get_image_overlays to get images of the specified marker channels that are then used to prepare the final image overlay in the style of the Visualizer * get_xy_tiles, concatenate_visualizer_tiles, and define_image_window have been moved from SpatialMap to emconnect * In addition, the new plotImage.Region2 is a slightly more generalized version of plotImage.Region, which instead takes an acquisition ID instead of a SpatialMap Region object

SpatialMap 0.4.60

• Add ability to specify markers when running QCMetrics

SpatialMap 0.4.59

• Added User Journey Analysis Guide 4 (Subsetting and subclustering)

SpatialMap 0.4.58

• Fix bugs in spatial qc workflow

SpatialMap 0.4.57

• making sure plotting functions and cohort comparison functions have a consistent terminology and logic for user
• Major updates to plotCellProportions so that it now includes the ability to choose plot type. See documentation for more details
• Updates to plotCohortsVolcano so that it’s output is more interpretable.
• compareCohorts being more robust

SpatialMap 0.4.56

• Added User Journey Analysis Guide 3 (unsupervised clustering)

SpatialMap 0.4.55

• Add tick marks and QC settings as subtitle for plotQCSummary plots

SpatialMap 0.4.54

• Added description of QC uploads to vignettes for “Workbench User Journey”
• Updated uploadQC default create_explorer_output = FALSE

SpatialMap 0.4.53

• Added spatialQC function

SpatialMap 0.4.52

• Automatically rotate x-axis labels for plot_proportions() and plotCellProportions()

SpatialMap 0.4.51

• Adding the first batch of vignettes for the new “Workbench User Journey”
• Minor change to filter plotting functions for consistency with QC metric plotting functions
• Dropping suggest on quantable

SpatialMap 0.4.50

• Minor changes to plotImage.Region
  • Fix coordinate inversion when defining window
  • Changed composite operator from "add" to "plus"

SpatialMap 0.4.49

• Update to uploadCellMetadata: includes option to include associated quality_filter_id (QC annotation)

SpatialMap 0.4.48

• Updates to composite image preparation in plot.ImageRegion

SpatialMap 0.4.47

• Added functions compareCohorts and get_valid_metadata_counts
  • compareCohorts runs a t-test to compare differential abundance of cell types (or other metadata) between cohorts
  • get_valid_metadata_counts creates a frequency table for cell and project metadata variables, while exlcuding non-existant cohorts that plague just running table(...) on the data

SpatialMap 0.4.46

• Updates to uploadCellMetadata: include associated cell_type_annotation_id for cell_neighborhood_classification uploads; pass connection and schema to emconnect::determine_data_versions; minor changes to documentation

SpatialMap 0.4.45

• Updates to plotImage.Region to be compatible with recent changes in emconnect

SpatialMap 0.4.44

• Re-work annotation uploads to be clearer and more compatible with emconnect

SpatialMap 0.4.43

• Improvements to plot.ImageRegion, including ability to specify min/max threshold values and trim for each channel/marker. Deprecates min.val and max.val, which are instead given in the form of a list to a new parameter called rescale. This allows more intuitive entry of these values per marker (e.g. NULL can be given instead of c(min.val,max.val). The output plot also now includes text indicating the marker colors.

SpatialMap 0.4.42

• Minor update to resolve linting issues.

SpatialMap 0.4.41

• Allow upload of QC filters to Portal using uploadCellMetadata

SpatialMap 0.4.39

• added function load_sm_data(), which allows enable users to easily load SpatialMap example datasets

SpatialMap 0.4.38

• Added check for whether cells are present in the window given to plotImage.Region

SpatialMap 0.4.37

• A quick update to fix hardcoded mistakes in plotImage.Region and get_image
• mergeProjectMetadata() is now automatically run during spatialmap_from_db, as this behavior is more intuitive for most users.

SpatialMap 0.4.36

• Create pkgdown site

SpatialMap 0.4.35

• Updated robust_scale to divide by 1 when the MAD is 0

SpatialMap 0.4.34

• Fixed a bad plot in the intro vignette

SpatialMap 0.4.33

• updated MR checklist

SpatialMap 0.4.32

• Fixes to getCellInteractions $interaction_name output
• Added an argument directed_edges to getCellInteractions that lets user choose whether edges are 1 or 2-way

SpatialMap 0.4.31

• New function getCellInteractions returns an explicit list of all cell-cell interactions

SpatialMap 0.4.30

• add ggrepel

SpatialMap 0.4.29

• Fixed vignette builds and cleaned them up a bit
• Fixed strange issue arising in check() for S4 methods. Probably a roxygen bug.
• Reestablished devtools in CI

SpatialMap 0.4.28

• Get rid of weird method dispatch warning/note

SpatialMap 0.4.27

• Make Repair more robust and intuitive in different situations, e.g., it doesn’t do anything to objects that are current.
• Moved Seurat and STvEA integrations off-line
• Again some file organization: AllClasses.R and AllGenerics.R added.

SpatialMap 0.4.26

• Fix NA handling in plotExpressionHeatmap

SpatialMap 0.4.25

This update carries major updates to Nearest Neighbor (NN) objects and spatial analyses. Some breaking changes may have been introduced.

Neighbors, Graphs, and Spatial Analyses

Plotting and Visualization

• Users can now plot cell neighborhood compositions in a facet style with plotNeighborhoodCellCounts
• Plotting NN graph representations is now possible in plotRepresentation! Use graph = "..." with the NN name to layer your network graph on the plot.
• Pairwise adjacencies can now be plotted as volcano plots
• Rather than invert Y coordinates on the fly every time, which is confusing, Y coordinates are inverted on download with emconnect. Plotting older objects will be weird! This can be updated with Repair() as usual, though.

Methods and Computations

• A function to calculate local Shannon entropy over a graph has been added: localEntropy
• A function to quantify the degree to which a particular cell-cell interaction occurs has been added: infiltrationScore
• A method to add self interactions and retrieve NN names

Internals

• Generics and their methods have been reviewed and cleaned up where issues arose
• nearestNeighborGraphs slot is renamed to graphs
• Cell neighborhoods take self into account by default. The opposite is true for pairwise adjacency computations.
• Complete re-work (and improvement) of pairwiseAdjacency internals
• Re-work interactions vignette

General package changes

• Clean & update sm_skin and sm_tonsil example datasets
• Substantial updates to names, cells, and Representations methods
• We now import purrr. A big decision but a necessary one for performance reasons. Over time many apply could be phased out.

Minor changes

• Fixed a stupid logic bug in createRegionObject, which silently causes corruption of cellMetadata
• … Many other bug fixes and adjustments
• Renamed poorly named functions
• Removed older, unused functions
• Reorganized files

SpatialMap 0.4.24

• Very minor updates to Repair and its documentation

SpatialMap 0.4.23

• Add logit-transformed cell interaction proportions to compareAdjacency
• Generally update NN methods to be cleaner and correct
• Added method slot to NN class
• Added consistent methods for NN class - plus many new functions
• Documentation sweep
• Full cell interaction vignette.

SpatialMap 0.4.22

• Change emconnect names in line with emconnect 1.2.0
• Fixed a bug with embeddings that caused plotRepresentation to fail
• added ... parameter to allow analyze = to be set
• .smapply checks returns now and gives a helpful error message in some cases
• Vignette name changes to make them easier to access

SpatialMap 0.4.21

• Minor bugs fixed:
  • Neighborhood clustering helper function subsampling error
  • Seurat to SpatialMap conversion error when Region names come from factors
  • Fixed issues with package documentation

SpatialMap 0.4.20

• Remove basilisk (python environment option)
• Updated logos & schematics
• Added package documentation (package?SpatialMap) with refs to vignettes
• Fixed a bug in plotImage causing misarranged tiles at higher zooms
• emconnect IO:
  • emconnect::get_biomarker_data2 to get_biomarker_data
  • Expose ds parameter

SpatialMap 0.4.19

• Updated vignettes.
  • Manipulating SpatialMap Objects
  • Accessing SpatialMap Data
• Resolved issues and bugs discovered during vignette writing.
  • export runPCA
  • fixed bug where cellMetadata-SpatialMap-method dropped columns
  • fixed problematic dup col removal in createRegionObject
  • Fix extra NA category in default_color_scale
  • Fix default legend for continuous scales
  • Added NNs and Representations methods for SpatialMap
  • Several more minor issues
• plotImage works again after adjustments to emconnect and DB from the Eng team

SpatialMap 0.4.18

• Fixed issues with Normalize when MARGIN paremeter differed from default.

SpatialMap 0.4.17

• Fixed an error where features<- would break expecting a @featureInfo slot in SpatialMap
• Fixed a major error introduced in 0.4.16 where Analyses would be wiped out by subsetting
  • Subsetting was added to all smapply calls in 0.4.16 so Analyses were always wiped out.

SpatialMap 0.4.16

• Add additional Portal version information to SpatialMap pulls
• Made it so uploadCellMetadata checks the DB for missing cells (and fills with NA if you choose) - then reverted the change, as Munchlax will handle that on Enable Portal
• QoL added 64+ color palettes
• Cleaned up nearest neighbors code
• Added Delaunay Triangulation to possible nearest neighbors methods
• Avoiding errors resulting from .smsubset and combineMaps
• Fixed an error where spatial embeddings() would not retrieve from SpatialMap

SpatialMap 0.4.15

• Significant updates to splitting, subsetting, and combining objects:
  • Added combineMaps function, which combines a list of SpatialMaps
  • Added a draft general-purpose SM subset function .smsubset()
  • Allowed Regions to be subset with zero cells, returning NULL.
  • Major bugfix to how .smc() was combining Representations and nearestNeighborGraphs.
    • (Specifically, both slots are enforced to be a list of the proper S4 objects (if not NULL). Grouping with .smc() was erroneously creating nested lists).
    • Also added a validity check around this idea.
  • Extract a Region using numeric / character index and R double brackews [[
• Minor changes:
  • createAnalysis() now has default arguments for the most common use cases
  • createRegionObject() no longer always creates a spatial Representation. Exposed arg.
  • Re-worked PCA and UMAP for clarity and consistency.
  • Added get_image . This still needs more thought.
  • Added cellMetadata-set-SpatialMap method (cellMetadata<-)
  • cellMetadata factor levels are automatically dropped on subset
• Cache package installs prior to build.

SpatialMap 0.4.14

• Added two features to Normalize(): custom arbitrary functions, and min-max scaling
• Improved clustering implementations & interface
• Fixed bugs in plotImage
• Added getImage function
• Fixed bugs in uploadCellMetadata()
• Added Pkgdown docs
• Patch to broken grouped analysis: fixed a bug in .smsplit() where only the first group’s Regions were analyzed

SpatialMap 0.4.13

• Finalized new Region-combine logic - comes with a much sleeker Utils file, and the ability to arbitrarily combine Regions on the fly by metadata.
• Various bug fixes, clean-ups, and aesthetic changes

SpatialMap 0.4.12

• Added a helper function to subset Regions by coordinate
• Made the included data much smaller, and removed the Seurat data
• Updated the vignette
• Fixed bug in plotViolin() function
• Resolved issues with cellMetadata initialization and propagation in the createRegionObject() function. Need to continue to monitor behavior here.
• Prevent NA cell_ids when cells lacked entries in cell_annotations
• Made extensive documentation fixes
• R CMD check at zero warnings.
• Removed S3 interface, moved that to emconnect
• .smapply based plotting functions (e.g., plotting spatial Representations; QC plots) now return lists of plots. User can handle composing them.

SpatialMap 0.4.11

• Added a NEWS.md file to track changes to the package.
• Added the differentialExpression() and neighborhoodClusters() functions. The latter computes cell neighborhoods from a nearest-neighbor network, and automatically clusters the result using K-means clustering, optimizing the number of clusters using the silhouette score.
• Added functions to visualize cell neighborhoods
• Added support for downloading general cell annotations from Enable Portal into cellMetadata() (via emconnect). Specifically, “IO.R” pulls from the cell_annotations branch of DB tables.
• Reorganized code into more proper file locations.
• Made changes to CI, which still does not quite work, but fixing this is out of scope for this version.