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()
.
Development version on Bioconductor 3.19.
SIGNIFICANT USER-VISIBLE CHANGES
- Added a new argument
margin_dist
fordefine_structure()
. Specifying the margin width with microns instead of layers of cells.
BUG FIXES
- Added legends to
plot_cell_categories()
plots whenlayered = TRUE
. - Added a distance parameter to fix the dimension error in
calculate_spatial_autocorrelation()
.
SIGNIFICANT USER-VISIBLE CHANGES
- Fixed thresholding bug in
predict_phenotypes()
.
NOTES
- Added Shiny App (reading data) link.
NOTES
- Fixed typo in citation and SPIAT overview diagram.
- Moved the following packages from Imports to Suggests: alphahull, plotly.
- Added citation to the newly published paper.
Development version on Bioconductor 3.18.
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.
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 parametersn_of_polygons
anddraw
.
NOTES
- Moved the following packages from Imports to Suggestions: graphics, umap, Rtsne, rlang, ComplexHeatmap and elsa. SpatialExperiment requires version >= 1.8.0. Removed xROI.
BUG FIXES
- Fixed error when there are only one cell in the clusters. (
identify_neighborhoods()
).
BUG FIXES
- The calculation of cell types of interest to
All_cells_in_the_structure
incalculate_proportions_of_cells_in_structure()
was incorrect. Now fixed.
SIGNIFICANT USER-VISIBLE CHANGES
- Re-organised the vignettes.
BUG FIXES
- Fix bug when Cell.ID column is missing from the spe_object in
identify_neighborhood()
.
Development version on Bioconductor 3.17.
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).
BUG FIXES
- Minor bug in
average_nearest_neighbor_index()
- the variableoutput
was not defined when there is no reference cell found in the image.
SIGNIFICANT USER-VISIBLE CHANGES
average_nearest_neighbor_index()
now returns the index along with the pattern type and the p value.
BUG FIXES
- Renamed the file of
R_BC()
. - Fixed a minor bug in
identify_bordering_cells()
that causes error.
SIGNIFICANT USER-VISIBLE CHANGES
mixing_score_summary()
ensures returning data in any situation. There will be difference between returningNA
and0
. See updated documentation.
BUG FIXES
- Fixed
format_image_to_spe()
"general" format. Assigned rownames (markers) and colnames (Cell IDs) to the assay of the formatted spe object.
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.
BUG FIXES
- Fixed formatting image error when
intensity_matrix
is NULL under "general" option.
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()
, andplot_distance_heatmap()
.
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:
identify_bordering_cells()
- deleted "tumour" from the plot title;plot_cell_categories()
- cell categories changed to not contain "immune" whenfeature_colname == "Structure"
;calculate_distance_to_tumour_margin()
renamed tocalculate_distance_to_margin()
;R_BT()
renamed toR_BC()
;calculate_summary_distances_of_cells_to_borders()
- one column in the returned data frame has name change;defined_strcture()
- parametername_of_immune_cells
renamed tocell_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 sendingERROR
when the cells of interest do no form any clusters.
BUG FIXES
- Fixed internal function
bind_info()
to avoid duplicated columns.
BUG FIXES
- Added checks for
dimensionality_reduction_plot()
to return error when the cell count in an image is too low.
SIGNIFICANT USER-VISIBLE CHANGES
- Added
perplexity
parameter todimensionality_reduction_plot()
. - Added
plot_final_border
parameter toidentify_bordering_cells()
.
BUG FIXES
image_splitter()
returnsNULL
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
incalculate_proportions_of_cells_in_structure()
was incorrect. Now fixed.
SIGNIFICANT USER-VISIBLE CHANGES
- Updated the main object class from
SingleCellExperiment
toSpatialExperiment
. - Replace "sce" with "spe" in function names.
- Reading data by
format_image_to_spe()
usinggeneral
format is recommended. For other data platforms,format_inform_to_spe()
,format_halo_to_spe()
,format_codex_to_spe()
, andformat_cellprofiler_to_spe()
are also available. - Deleted "Visium" format option in
format_image_to_spe()
. image_splitter()
now returns a list of spe objects.
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.
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.
- Version for the paper submitted to BioRxiv.