Changelog

Source: NEWS.md

SPIAT 1.4.2

• Fixed the wrong layering in plot_cell_categories() and added legend when layer=TRUE.

SPIAT 1.4.1

BUG FIXES

• No error message when there are duplicates generated by the TSNE option of dimensionality_reduction_plot() function.
• Deleted duplicated plots returned by plot_cell_categories().

SPIAT 1.4.0

Release version on Bioconductor 3.18.

SPIAT 1.3.5

SIGNIFICANT USER-VISIBLE CHANGES

• Added a new argument margin_dist for define_structure(). Specifying the margin width with microns instead of layers of cells.

SPIAT 1.3.4

BUG FIXES

• Added legends to plot_cell_categories() plots when layered = TRUE.
• Added a distance parameter to fix the dimension error in calculate_spatial_autocorrelation().

SPIAT 1.3.3

SIGNIFICANT USER-VISIBLE CHANGES

• Fixed thresholding bug in predict_phenotypes().

NOTES

• Added Shiny App (reading data) link.

SPIAT 1.3.2

NOTES

• Fixed typo in citation and SPIAT overview diagram.
• Moved the following packages from Imports to Suggests: alphahull, plotly.

SPIAT 1.3.1

• Added citation to the newly published paper.

SPIAT 1.3.0

Development version on Bioconductor 3.18.

SPIAT 1.1.6

BUG FIXES

• Fixed the mixing score and normalised mixing score calculation. Each reference-reference interaction is now counted once (was treated directional and counted twice) and the fraction of normalised mixing score is fixed.

SPIAT 1.1.5

SIGNIFICANT USER-VISIBLE CHANGES

• Return message instead of error when there are no cells of interest present in the image (identify_neighborhoods()).
• Removed the option of manually defining tumour regions in identify_bordering_cells(). Removed parameters n_of_polygons and draw.

NOTES

• Moved the following packages from Imports to Suggestions: graphics, umap, Rtsne, rlang, ComplexHeatmap and elsa. SpatialExperiment requires version >= 1.8.0. Removed xROI.

SPIAT 1.1.4

BUG FIXES * Fixed error when there are only one cell in the clusters. (identify_neighborhoods()).

SPIAT 1.1.3

BUG FIXES * The calculation of cell types of interest to All_cells_in_the_structure in calculate_proportions_of_cells_in_structure() was incorrect. Now fixed.

SPIAT 1.1.2

SIGNIFICANT USER-VISIBLE CHANGES

• Re-organised the vignettes.

SPIAT 1.1.1

BUG FIXES * Fix bug when Cell.ID column is missing from the spe_object in identify_neighborhood().

SPIAT 1.1.0

Development version on Bioconductor 3.17.

SPIAT 0.99.14

BUG FIXES

• Fixed bugs in identify_neighborhoods():

1. Assign “Free_cell” to the cells of interest when the number of clustered cells are smaller than min_cluster_size in each cluster;
2. Fixed spe_object output (Adding “Neighborhood” column had a bug previously).

SPIAT 0.99.13

BUG FIXES

• Minor bug in average_nearest_neighbor_index() - the variable output was not defined when there is no reference cell found in the image.

SPIAT 0.99.12

SIGNIFICANT USER-VISIBLE CHANGES

• average_nearest_neighbor_index() now returns the index along with the pattern type and the p value.

SPIAT 0.99.11

BUG FIXES

• Renamed the file of R_BC().
• Fixed a minor bug in identify_bordering_cells() that causes error.

SPIAT 0.99.10

SIGNIFICANT USER-VISIBLE CHANGES

• mixing_score_summary() ensures returning data in any situation. There will be difference between returning NA and 0. See updated documentation.

SPIAT 0.99.9

BUG FIXES

• Fixed format_image_to_spe() “general” format. Assigned rownames (markers) and colnames (Cell IDs) to the assay of the formatted spe object.

SPIAT 0.99.8

BUG FIXES

• Fixed format_image_to_spe() “general” format. The NA intensity value removal was for markers. Instead, it should remove cells that have NA marker intensities.
• Fixed predict_phenotypes() plot error.

SPIAT 0.99.7

BUG FIXES

• Fixed formatting image error when intensity_matrix is NULL under “general” option.

SPIAT 0.99.6

SIGNIFICANT USER-VISIBLE CHANGES

• identify_bordering_cells() emit Warning when no bordering cells are detected.

BUG FIXES

• Fixed the message displayed for NA removal when formatting image using “general” format.
• Fixed plot functions to display only one plot. plot_marker_level_heatmap(), and plot_distance_heatmap().

SPIAT 0.99.5

SIGNIFICANT USER-VISIBLE CHANGES

• Generalised functions in tumour structure families to suit other tissue and cell types, not restricted to tumour and immune cells. The affected functions include:
  1. identify_bordering_cells() - deleted “tumour” from the plot title;
  2. plot_cell_categories() - cell categories changed to not contain “immune” when feature_colname == "Structure";
  3. calculate_distance_to_tumour_margin() renamed to calculate_distance_to_margin();
  4. R_BT() renamed to R_BC();
  5. calculate_summary_distances_of_cells_to_borders() - one column in the returned data frame has name change;
  6. defined_strcture() - parameter name_of_immune_cells renamed to cell_types_of_interest;
• identify_bordering_cells() can return the number of clusters of the specified cell type.

BUG FIXES

• Fixed the calculation of the normalised cross-K AUC in AUC_of_cross_funcion().
• identify_neighborhood() returns an SPE object instead of sending ERROR when the cells of interest do no form any clusters.

SPIAT 0.99.4

BUG FIXES

• Fixed internal function bind_info() to avoid duplicated columns.

SPIAT 0.99.3

BUG FIXES

• Added checks for dimensionality_reduction_plot() to return error when the cell count in an image is too low.

SPIAT 0.99.2

SIGNIFICANT USER-VISIBLE CHANGES

• Added perplexity parameter to dimensionality_reduction_plot().
• Added plot_final_border parameter to identify_bordering_cells().

BUG FIXES

• image_splitter() returns NULL for the sub-images that do not contain any cells.
• calculate_spatial_autocorrelation()
• identify_bordering_cells() only plots the bordering cells when bordering cells are detected and the user chooses to plot them.
• The calculation of one cell type to All_cells_in_the_structure in calculate_proportions_of_cells_in_structure() was incorrect. Now fixed.

SPIAT 0.99.1

SIGNIFICANT USER-VISIBLE CHANGES

• Updated the main object class from SingleCellExperiment to SpatialExperiment.
• Replace “sce” with “spe” in function names.
• Reading data by format_image_to_spe() using general format is recommended. For other data platforms, format_inform_to_spe(), format_halo_to_spe(), format_codex_to_spe(), and format_cellprofiler_to_spe() are also available.
• Deleted “Visium” format option in format_image_to_spe().
• image_splitter() now returns a list of spe objects.

SPIAT 0.99.0

Version submitted to Nature Communications. Access the release v0.99.0 here.

SIGNIFICANT USER-VISIBLE CHANGES

• Systematically renamed parameter names. For example, the parameter for selecting a column of interest is changed from “column” to “feature_colname”.
• Added a function entropy_gradient_aggregated() for calculating cell colocalisation.
• Added a function dimensionality_reduction_plot() for visualisation and quality control.
• Added examples to documentation. The example datasets were simulated by spaSim.

SPIAT 0.4

SIGNIFICANT USER-VISIBLE CHANGES

• Added a new parameter “column” to most functions to select a column of interest.
• Users can define cell types based on certain marker combinations or cell properties.
• Improved tumour border detection (identify_bordering_cells()).
• Added functions to define tumour structure and characterise immune populations in different tissue regions.
• Added functions to characterise spatial heterogeneity.
• Added functions for cell colocalisation, including mixing score, normalised mixing score, cross K function.

SPIAT 0.2

• Version for the paper submitted to BioRxiv.