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specs.md

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Specs for insitutypeML:

  • Returns a vector of cell type assignments -- test: test_insitutype.R#L54
  • Returns a vector of posterior probabilities / confidence scores -- test: test_insitutype.R#L55
  • Returns a matrix of cell * cell type log-likelihoods -- test: test_insitutype.R#L56
  • Returns a matrix of cell type profiles -- test: test_insitutype.R#L57

Specs for insitutype:

  • If run with fixed_profiles and 0 new clusters, produces valid outputs:
    • Returns a vector of cell type assignments -- test: test_insitutype.R#L82
  • Returns a vector of posterior probabilities / confidence scores -- test: test_insitutype.R#L83
  • Returns a matrix of cell * cell type log-likelihoods -- test: test_insitutype.R#L84
  • Returns a matrix of cell type profiles -- test: test_insitutype.R#L85
  • If run with no fixed_profiles (fully unsupervises), produces valid outputs:
    • Returns a vector of cell type assignments -- test: test_insitutype.R#L112
  • Returns a vector of posterior probabilities / confidence scores -- test: test_insitutype.R#L113
  • Returns a matrix of cell * cell type log-likelihoods -- test: test_insitutype.R#L114
  • Returns a matrix of cell type profiles -- test: test_insitutype.R#L115
  • If unsupervised clustering is run with initial clusters specified, produces valid outputs:
    • Returns a vector of cell type assignments -- test: test_insitutype.R#L144
  • Returns a vector of posterior probabilities / confidence scores -- test: test_insitutype.R#L145
  • Returns a matrix of cell * cell type log-likelihoods -- test: test_insitutype.R#L146
  • Returns a matrix of cell type profiles -- test: test_insitutype.R#L147
  • The clusters returned have the same names as the initial clusters -- test: test_insitutype.R#L148
  • If semi-supervised clustering is run with initial clusters specified, produces valid outputs:
    • Returns a vector of cell type assignments -- test: test_insitutype.R#L177
  • Returns a vector of posterior probabilities / confidence scores -- test: test_insitutype.R#L178
  • Returns a matrix of cell * cell type log-likelihoods -- test: test_insitutype.R#L179
  • Returns a matrix of cell type profiles -- test: test_insitutype.R#L180

Specs for updateReferenceProfiles:

  • Returns a matrix of new profiles -- test: test_insitutype.R#L316
  • Returns a vector of anchor assignments -- test: test_insitutype.R#L317

Specs for refineClusters:

  • Merging operations happen correctly -- test: test_insitutype.R#L196
  • Cell names are preserved -- test: test_insitutype.R#L196
  • Makes no changes if none are requested -- test: test_insitutype.R#L302
  • Merging operations happen correctly if merges and deletions are asked for -- test: test_insitutype.R#L307
  • Merging operations happen correctly if merges are asked for -- test: test_refinecells_cell_merging_logic.R#L14,18,22

Specs for chooseClusterNumber:

  • Returns a single value for "best cluster number" -- test: test_insitutype.R#L219
  • Reports the cluster numbers considered -- test: test_insitutype.R#L220
  • Reports the log likelihood from each cluster number #221
  • Reports the AIC from each cluster number #222
  • Reports the BIC from each cluster number #223

Specs for get_anchor_stats

  • Returns a matrix of cosine distances -- test: test_insitutype.R#L236
  • Returns a matrix of log likelihood ratios -- test: test_insitutype.R#L237

Specs for choose_anchors_from_stats

  • Assigns values consistent with the cell type names of the inputs -- test: test_insitutype.R#L253
  • Assigns no more than the specified number of anchors per cell type -- test: test_insitutype.R#L253
  • The anchors vector aligns to the rows of the counts matrix (cells) -- test: test_insitutype.R#L254

Specs for find_anchor_cells

  • Assigns values consistent with the cell type names of the inputs -- test: test_insitutype.R#L271
  • Assigns no more than the specified number of anchors per cell type -- test: test_insitutype.R#L272
  • The anchors vector aligns to the rows of the counts matrix (cells) -- test: test_insitutype.R#L273
  • Returns NULL if no cells meet anchor criteria -- test: test_insitutype.R#L288

Specs for flightpath_layout

  • Returns correctly formatted results:
    • Cluster positions are in a 2-column matrix -- test: test_flightpath.R#L34
  • Cell positions are in a 2-column matrix -- test: test_flightpath.R#L35
  • There are no missing cluster positions -- test: test_flightpath.R#L36
  • There are no missing cell positions -- test: test_flightpath.R#L37

Specs for flightpath_plot

  • when passed a result from flightpath_layout, flightpath_plot returns a ggplot object -- test: test_flightpath.R#L43
  • when passed an insitutype results, flightpath_plot returns a ggplot object -- test: test_flightpath.R#L51
  • when asked to show meanConfidence, flightpath_plot returns a ggplot object -- test: test_flightpath.R#L57

Specs for fastCohorting

  • Returns a vector of cohort assignments -- test: test_insitutype.R#L325
  • Returns the specified number of unique cohorts -- test: test_insitutype.R#L325