Changelog

v3.0.1

Release date: 2023-06-20

Added

• assay._Assay.crosstab() to wrap pandas.crosstab for ease of use with mosaic.

• assay._Assay.crosstabmap() to create heatmaps of the output of assay._Assay.crosstab().

• assay._Assay.hierarchical_cluster() to get the hierarchical clustering order of the rows of a DataFrame.

Changed

• Updated matplotlib dependency from <=3.2.2 to >=3.4.0

Fixed

• assay._Assay.heatmap() subclustering performed when convolve=0. It was disabled by default.

• Custom typography.css used in workflows is included in the package data

• Setting labels using dictionaries in assay._Assay.set_labels().

v3.0.0

Release date: 2023-06-16

Added

• A wrapper for COMPASS.

• New variant filters that account for missing data.

• Recipe and instructions for building installers.

• plot_kind parameter to dna.Dna.group_by_genotype() to change the type of plot shown.

• filter_cells to io.load() which loads only the intersection algorithm cells.

• Progress bar to io.load()

• algorithms.nsp.NSP and algorithms.nsp.ExpressionProfile to modularize the NSP code.

• x_groups to assay._Assay.heatmap() to group the x-axis by a given list of ids.

• Simplify and speedup assay._Assay.heatmap() by removing duplicate data. (By using plots.heatmap.Heatmap)

• assay._Assay.convolve() to convolve the data that was earlier performed in the Heatmap.

• Configuration options accessible via Config:

  • ms.Config.Colorscale.Dna to change the default color palette for all DNA plots.

  • ms.Config.Colorscale.Cnv to change the default color palette for all CNV plots.

  • ms.Config.Colorscale.Protein to change the default color palette for all Protein plots.

• Custom divirgent colorscale for Cnv Ploidy heatmaps

• Option to return indices instead of barcodes in assay._Asasy.clustered_barcodes().

• sample.Sample.common_barcodes() to get the common barcodes across assays.

• Add subcluster paramter to assay._Assay.clustered_barcodes() to prevent clustering within the labels

• Option to pass n-dimensional arrays as splitby in assay._Assay.clustered_barcodes()

• Option to fetch a subset of the assays in sample.Sample.assays() using the names parameter

• sample.Sample.clustered_barcodes() to hierarchically cluster using multiple assays

• Multiple options added to sample.Sample.heatmap() to sort the assays, barcodes, and the features

• assay._Assay.signature`() accepts a splitby parameter to get the signature for each unique label in splitby.

• Improvements to assay._Assay.signaturemap():

  • labels and ids are clustered by default.

  • Option to pass a list of labels to assay._Assay.signaturemap() to order the labels.

  • The default features option for cnv.Cnv.signaturemap() is set to positions.

• Option to copy the labels and palette together by passing an assay._Assay() to assay._Assay.set_labels()

• assay._Assay.heatmap() sets subcluster=False when calculating the barcode order when convolve is provided.

• Varsome URLs as hyperlinks on the variant name in the VariantSubcloneTable

• Add percentage of cells and amplicons present to the CopyNumberWorkflow

• dna.Dna.mutated_cells() to get the number of cells with at least 1 mutation in each given clone. This is used in sample.Sample.signaturemap().

Changed

• apply_filter changed to filter_variants in io.load()

• SubcloneTree and SubcloneTreeGraph classes are renamed to Tree and TreeGraph respectively.

• show_plot to return_plot in dna.Dna.group_by_genotype()

• plots.heatmap.Heatmap splits the vertical and horizontal lines on the main heatmap into two traces.

• The default value of vaf_het in dna.Dna.filter_variants() changed from 35 to 30.

• Flattened sample.Sample.heatmap`() option has been removed. A more customizable version is available under the sample.Sample.signaturemap() function.

• The constant - constants.COLORS to have unique values.

  • The grey values at the 10th, 20th, 30th.. positions were modified to be unique

  • The black (#000000) value was moved from the 20th position to the last position

Fixed

• Get indexes maintains the order as per find_list when there are duplicates in the find_list and order_using_find_list is True.

• DANN score in the variants subclone table is shown correctly for saved h5 files.

• Overlapping of text in phylogeny trees.

• Error in multiprocessing when fetching gene_names for CNV by adding a max_workers parameter and using threads instead of processes.

• Missing clone is ignored when finding ADO sisters.

Removed

• Functions to convert legacy loom files to h5 files - io._loom_to_h5, io._update_file

• Functions to read data from csv files - io._merge_files, io._cnv_raw_counts, io._protein_raw_counts

• Function to merge h5 files - io._merge

• show_plot from protein.Protein.normalize_reads(). The same plot can be created in plotly using algorithms.nsp.NSP.plot()

• show_plot from protein.Protein.get_signal_profile(). The same plot can be created in plotly using algorithms.nsp.ExpressionProfile.plot()

• protein.Protein.get_signal_profile function. It can be executed using algorithms.nsp.ExpressionProfile.fit() if needed.

• protein.Protein.get_scaling_factor function. It can be executed using algorithms.nsp.NSP.scaling_factor() if needed