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Changelog

Ver. 1.1.2 (2023-03-22)

  • Fix minor bugs

Ver. 1.1.1 (2023-03-22)

  • Add a new tutorial Use user defined pseudotime
  • Fix minor bugs

Ver. 1.1.0 (2023-03-17)

  • Add a pseudotime parameter to cp.tl.dtw(), cp.tl.genes_similarity_score(), and cp.pl that enable users to use user-defined pseudotime in dynamic time warping
  • cp.tl.trajectory_tree() now accepts a user-preprocessed dataset
  • Fix minor bugs

Ver. 1.0.14 (2022-12-16)

  • Specify the matplotlib version as 3.5.2 due to errors in plotting figures

Ver. 1.0.13 (2022-07-23)

  • Fix minor bugs

Ver. 1.0.12 (2022-07-23)

  • Add multi_gene parameter to capital.pl.gene_expression_trend() so that users can plot a gene expression trend using results of multi genes calculated in capital.tl.dtw()
  • Fix minor bugs

Ver. 1.0.11 (2022-07-14)

  • Change function cp.tl.dpt() to calculate the root cell so that it is derived from all cells in the datasets and used for all linear alignments
  • Fix minor bugs

Ver. 1.0.10 (2022-07-05)

  • Fix minor bugs

Ver. 1.0.9 (2022-07-05)

  • Updated capital.tl.dtw()
  • Fix minor bugs

Ver. 1.0.8 (2022-06-28)

  • Specify the Networkx version as 2.8.3 due to errors in plotting figures
  • Fix minor bugs

Ver. 1.0.7 (2022-05-15)

  • Fix minor bugs

Ver. 1.0.6 (2022-05-15)

  • Fix compatibility with scanpy 1.9.1

Ver. 1.0.5 (2022-05-14)

  • Fix minor bugs
  • Delete synthetic_dataset1 and synthetic_dataset2 from capital.dataset function

Ver. 1.0.4 (2021-12-03)

  • Add some new arguments in plotting
  • Fix minor bugs

Ver. 1.0.3 (2021-10-08)

  • Adjust CAPITAL codes to the recent Scanpy update to 1.8.1
  • Fix minor bugs

Ver. 1.0.2 (2021-03-16)

  • Fine-tune codes to the Code Ocean compute capsule, changing the locations of directories for saving results

Ver. 1.0.1 (2021-03-03)

  • Specify the Scanpy version as 1.6 for pip installation to guarantee the reproducibility of results

Ver. 1.0.0 (2021-01-13)

  • Provide a brand new system so that one can use CAPITAL interactively, which is useful for the interactive development environment JupyterLab
  • Upload CAPITAL to PyPI to install it via 'pip' command
  • Upload a tutorial and API using a theme provided by Read the Docs
  • Upload datasets used in our work, which are available via CAPITAL's dataset functions
  • Improve running time
  • Fix minor bugs
  • Move early versions of CAPITAL to "legacy" directory

Ver. 0.2.3 (2020-11-13)

  • Add '--magic' option to impute gene expression data with MAGIC in pre_capital.py
  • Fix a minor bug in draw_capital.py
  • Improve calculation processes in all codes

Ver. 0.2.2 (2020-08-05)

  • Fix a bug for 10x Genomics data in capital.py
  • Replace '--local-align' option with '--no-prune' in capital.py
  • Add a new function for automatically saving figures on trajectory trees and their alignment in capital.py
  • Add a new positional argument <genes> in draw_capital.py, so that a user can input multiple genes all together
  • Add a new function for automatically saving figures on dynamic time warping and expression dynamics in the alignment directory generated with capital.py if a user does not specify where to save in draw_capital.py
  • Remove '--save' option in draw_capital.py, meaning that a figure file will be always saved
  • Remove '--showfig' option in draw_capital.py
  • Add x-label (and y-label) on plots generated with draw_capital.py
  • Adjust the layout of a figure legend to the figure area if --data1-name (--data2-name) is specified

Ver. 0.2.1 (2020-06-21)

  • Fix a bug on the process without cluster in capital.py
  • Fix a bug on the key error of leiden_colors in draw_capital.py

Ver. 0.2.0 (2020-06-01)

  • Adjust CAPITAL codes to the recent Scanpy update to 1.5
  • Add a function for 10x-MTX directory input in pre_capital.py

Ver. 0.1.14 (2020-05-15)

  • Improve the naming of the result directory with respect to gapcost in the tuning mode in capital.py

Ver. 0.1.13 (2020-05-08)

  • Change the data type of gapcost to float in capital.py
  • Keep the value of a gapcost in the result directory when the tuning mode is on in capital.py

Ver. 0.1.12 (2020-05-01)

  • Fix a bug in the statement on concatenation of AnnData in capital.py
  • Keep the name of a method for computing a tree in the result directory when the tuning mode is on in capital.py

Ver. 0.1.11 (2020-04-24)

  • Add '-p' option to specify the number of principal components to construct a nearest neighbor graph in pre_capital.py
  • Add '-M' option to specify the way of computing a minimum spanning tree (Euclid distance, adaptive Gaussian kernel or PAGA connectivity) in capital.py
  • Improve some processes for speed-up

Ver. 0.1.10 (2020-04-10)

  • Fix a bug on dynamic programing calculation in capital.py
  • Fix a bug on displaying a figure for tree alignment in capital.py

Ver. 0.1.9 (2020-02-15)

  • Compress output H5AD data generated with pre_capital.py and capital.py to save disk space
  • Disable output of H5AD data when '-t' option is used in capital.py
  • Change the hierarchy of generated aligned_data directory to remove redundancy
  • Fix a bug that occurs when no directory for saving figures is found in draw_capital.py
  • Change some option symbols in draw_capital.py for usability

Ver. 0.1.8 (2020-02-13)

  • Show the number of predicted clusters in standard out in pre_capital.py
  • Change the hierarchy of generated directories in capital.py
  • Improve the naming of result directories in the tuning mode in capital.py

Ver. 0.1.7 (2020-02-11)

  • Change part of option symbols in pre_capital.py and capital.py to avoid inconsistency between scripts as much as possible
  • Add a tuning mode in capital.py, which affects only naming of result directories

Ver. 0.1.6 (2020-02-10)

  • Improve a method for saving a PDF figure in pre_capital.py
  • Add a function for showing a progress bar when calculating dynamic time warping for each gene in capital.py
  • Change part of directories/files naming in capital.py

Ver. 0.1.5 (2020-02-07)

  • Fix a bug on print and change generated directories/files naming in capital.py

Ver. 0.1.4 (2020-02-03)

  • Fix a bug for the input of one aligned cluster pair in draw_capital.py

Ver. 0.1.3 (2020-02-02)

  • Add further explanations to help messages in pre_capital.py and draw_capital.py

Ver. 0.1.2 (2020-01-31)

  • Fix a bug on an attribute error associated with networkx in capital.py

Ver. 0.1.1 (2020-01-31)

  • Add a function for absolute paths input in capital.py
  • Allow multiple genes input in capital.py
  • Change the definition of a cluster centroid to a vector of the median of expression of each gene in the cluster
  • Add a function for showing normalized alignment distance
  • Fix a bug in traceback of tree alignment in capital.py

Ver. 0.1.0 (2020-01-21)

  • Add command line option parse
  • Split codes into pre_capital.py, capital.py and draw_capital.py

Ver. 0.0.2 (2019-12-05)

  • Fix a minor bug in capital.py

Ver. 0.0.1 (2019-11-29)

  • Upload capital.py for test use