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NEWS.md

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1.0.1

  • Modify the argument name from version="0.2.17 to version="0" to run SOM in the previous version.
  • Default output format of plotUMAP is changed from "pdf" to "png".
  • Modify labels of legend in distance map to discrete ones.

1.0.0

  • Add an option version to graphSOM and rxmcmc functions in order to enable us to perform SOM computations based on the previous version (= 0.2.17).

0.2.17

  • Add options size_d and size_s to plotDistMap function.
  • Add options color_by_group, grpcol, and magnify to plotUMAP function.

0.2.16

  • Replace graphSOM and rxmcmc functions of v.0.2.15 with those of v.0.2.14

0.2.15

  • Modify graphSOM function to guarantee the reproducibility between graphSOM and rxmcmc when the same seed value is given.
  • Add a new argument color_by_gene to the function plotUMAP.

0.2.14

  • Add rglclose option to plotUMAP function.

0.2.13

  • The umap package for plotUMAP function was replaced with uwot.

0.2.12

  • Update plotUMAP function. It supports 'png', 'pdf', and 'eps'.

0.2.11

  • Add 2D plotting option to plotUMAP.
  • Add scatterplot3d option to plotUMAP.

0.2.10

  • The output file names of writeMCMC function are changed.
  • The gene_size column is added to summary.txt.
  • Bugs are fixed.

0.2.9

  • Gibbs sampling strategy is introduced to the cluster swapping in GraphSOM.

0.2.8

  • The swap option is added to initGraphSOM function.
  • Thee seed options are added to selectFeatures, initGraphSOM, and rxmcmc functions.
  • Bugs are fixed.

0.2.7

  • selectFeatures() outputs NOT rejected genes.
  • Modify arguments of plotUMAP function.
  • Modify outputs format of RX-MCMC.

0.2.6

  • Bugs are fixed

espresso 0.2.4

  • The default value of the parameter maxRuns was changed from 1000 to 500 in selectFeatures function.
  • Rename variables rep to rept or repl.
  • Add max_ and min_ for score, acc, and ari to MCMC results.
  • Rename y-axis in MCMC plots.
  • Rename size to gene_size in MCMC results.

0.2.3

  • The default value of the parameter maxRuns was changed from 200 to 1000 in selectFeatures function.
  • The default value of the parameter coef was changed from 0 to 1.0 in initGraphSOM function.

0.2.2

  • Bugs are fixed

0.2.1

  • Bugs are fixed

0.0.2

  • Add rxmcmc function, which optimize gene sets by replica exchange MCMC approach.
  • Add plotMCMC function, which plots RX-MCMC results.
  • Add selectFeatures funtion, which selects feature genes by random forest based method Boruta.
  • Add plotDistMapfunction, which plots distance matrices between domains and between samples.

0.0.1

  • A beta-version of espresso is released.