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alexyermanos / Platypus

R package for the analysis of single-cell immune repertoires
GNU General Public License v3.0
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VDJ_Dynamics not recognizing feature column #35

Closed LBH2021 closed 1 year ago

LBH2021 commented 1 year ago

When I try to perform VDJ dynamics, I get the following error message (script and error message below). When I check the data frame columns, the designated column is present, and other repertoire dynamics functions such as VDJ_abundances and VDJ_ordination work using the same column.to.track input. Any help would be greatly appreciated. Thank you!

Tracks shared VDJ and VJ features across samples

  VDJ_dynamics(VDJ = TestVGM,
  • columns.to.track = 'VDJ_cdr3s_aa', #select which column in dataframe to track
  • timepoints.column = 'sample_id',
  • proportions.level = 'absolute.counts',
  • track.only.common = T) Error in VDJ_dynamics(VDJ = TestVGM, columns.to.track = "VDJ_cdr3s_aa", : Please provide valid feature column name(s) contained within VDJ
tudorcotet commented 1 year ago

Hi! Sorry for the late reply!

The VDJ_dynamics takes as input the VDJ part of the VGM object - VGM[[1]]. The error above is most likely due to having the whole VGM object as input, instead of the VDJ. Calling VDJ_dynamics with VDJ = TestVGM[[1]] should fix your issue!

We are planning to standardize the inputs for all Platypus functions to be the VGM object!