NEWS

SPIAT 1.7.2

BUG FIXES

Fixed cluster assignment issue in function identify_neighborhoods().

SPIAT 1.7.1

BUG FIXES

Added feature_colname parameter to functions plot_cell_marker_levels() and marker_intensity_boxplot().

SPIAT 1.7.0

Development version on Bioconductor 3.20.

SPIAT 1.5.3

BUG FIXES

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

SPIAT 1.5.2

NOTES

plot_cell_percentages() now returns the plot.

SPIAT 1.5.1

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 1.5.0

Development version on Bioconductor 3.19.

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():

Assign "Free_cell" to the cells of interest when the number of clustered cells are smaller than min_cluster_size in each cluster;
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.