RoheLab/vsp

Issues

• Bug: recentering and rescaling need to happen before heuristic column alignment

  #73 opened 5 months ago by alexpghayes
  0

• Bug: recentering seems to be broken

  #72 opened 5 months ago by alexpghayes
  0

• How to project new data using existing VSP loadings?

  #68 opened 2 years ago by ravwojdyla
  13

• [Suggest] Provide an option to re-order the columns of output Y

  #55 opened 2 years ago by fchen365
  7

• How to handle non/weak-diagonal hat_B?

  #69 opened 2 years ago by ravwojdyla
  11

• Release vsp 0.1.0

  #67 opened 3 years ago by alexpghayes
  0

• Some utilities to add

  #21 opened 3 years ago by alexpghayes
  1

• convert Z and Y to matrix?

  #66 opened 3 years ago by karlrohe
  2

• plot_svd_v and _u sample with leverage

  #65 opened 3 years ago by karlrohe
  1

• More diagnostic plots

  #42 opened 3 years ago by alexpghayes
  0

• Datasets

  #40 opened 5 years ago by alexpghayes
  2

• Subsetting to particular quantile of degree in varimax calculation

  #30 opened 3 years ago by alexpghayes
  1

• tidy() methods for embeddings?

  #62 opened 3 years ago by alexpghayes
  2

• should default to scale = T

  #64 opened 3 years ago by karlrohe
  1

• Implement inverse participation based diagnostics

  #20 opened 3 years ago by alexpghayes
  1

• tidy text integration

  #34 opened 3 years ago by karlrohe
  1

• Pairs plot should only calculate leverages for dimensions of interest

  #23 opened 3 years ago by alexpghayes
  0

• Can't install on Mac OS due to missing Open MP support in default compiler

  #63 opened 4 years ago by karlrohe
  7

• remove B from default?

  #36 opened 4 years ago by karlrohe
  3

• Trouble installing due to Open MP dependency on MacOS

  #59 opened 4 years ago by carolliu42
  2

• bad ylim with screeplot for normalize = F

  #35 opened 4 years ago by karlrohe
  0

• Add tests for matrix scale consistency

  #46 opened 4 years ago by karlrohe
  0

• Use an experimental branch

  #47 opened 4 years ago by alexpghayes
  4

• refactoring a bit for pairs plots

  #58 opened 4 years ago by karlrohe
  2

• [Suggest] add option to turn on/off the "normalize" in varimax rotation

  #60 opened 4 years ago by fchen365
  2

• Nearest neighbors in embedding space

  #61 opened 4 years ago by alexpghayes
  0

• defaults to vsp.matrix

  #56 opened 4 years ago by karlrohe
  1

• varimax pairs

  #57 opened 4 years ago by karlrohe
  0

• [Error] Cannot install the package

  #53 opened 4 years ago by fchen365
  2

• [Bug] parameters not passed

  #54 opened 4 years ago by fchen365
  0

• rotate U and V together to make B diagonal.

  #45 opened 4 years ago by karlrohe
  2

• Use implicit centering

  #29 opened 4 years ago by alexpghayes
  0

• Add option to decenter

  #33 opened 4 years ago by alexpghayes
  0

• Skew correction needs to apply to B as well as Y and Z

  #48 opened 4 years ago by alexpghayes
  0

• Get Fan's BFF function with vsp objects

  #27 opened 4 years ago by alexpghayes
  1

• Do the whole skew-positive thing

  #28 opened 4 years ago by alexpghayes
  0

• Figure out issue with signs in B

  #39 opened 4 years ago by alexpghayes
  3

• Improve the screenplot

  #41 opened 4 years ago by alexpghayes
  0

• return Z and Y as matrix not Matrix

  #49 opened 4 years ago by karlrohe
  0

• vsp(A,5) should run vsp(A,k=5)

  #50 opened 4 years ago by karlrohe
  0

• Is RSpectra::eigs() more efficient than RSpectra::svds() for symmetric matrices?

  #31 opened 5 years ago by alexpghayes
  4

• A better approach to centering

  #44 opened 5 years ago by alexpghayes
  2

• Update function to *reduce* k

  #43 opened 5 years ago by alexpghayes
  0

• import row/column names from A

  #38 opened 5 years ago by karlrohe
  1

• if A has negative elements

  #37 opened 5 years ago by karlrohe
  1

• UMAP visualization?

  #26 opened 5 years ago by alexpghayes
  1

• Care with eigenvector selection for unnormalized A

  #25 opened 5 years ago by alexpghayes
  0

• Add best feature function implementation that accepts vsp objects as input

  #24 opened 5 years ago by alexpghayes
  1

• Convergence diagnostics plots

  #19 opened 5 years ago by alexpghayes
  1

• Improvements to default print method

  #32 opened 5 years ago by alexpghayes
  0