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specs.md

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Specs for insitucor:

expect_identical(colnames(res$modules), c("module", "gene", "weight")) expect_true(nrow(res$scores_env) == nrow(counts)) expect_true(nrow(res$scores_sc) == nrow(counts)) expect_true(is(res$condcor, 'sparseMatrix')) expect_true(is.matrix(res$celltypeinvolvement)) expect_true(is.matrix(res$attributionmats[[1]]))

  • Returns a matrix of environment scores aligning to counts -- test: unit_tests.R#L48
  • Returns a matrix of single cell scores aligning to counts -- test: unit_tests.R#L49
  • Returns a sparse matrix of conditional correlations -- test: unit_tests.R#L50
  • Returns a matrix of cell type vs module attribution stats -- test: unit_tests.R#L51
  • Returns a list of matrices holding cell type vs gene attribution stats -- test: unit_tests.R#L52

Specs for calcSpatialCor:

  • Returns a sparse matrix holding conditional correlations -- test: unit_tests.R#L128,131
  • Returns a matrix of environment expression values -- test: unit_tests.R#L129,132
  • Returns a sparse matrix of neighbor relationships -- test: unit_tests.R#L130,133

Specs for defineModules:

  • Returns a list of module memberships -- test: unit_tests.R#L144,145
  • Returns a list of module weights -- test: unit_tests.R#L146,147
  • Returns a data frame summarizing weights and memberships -- test: unit_tests.R#L148

Specs for scoreModules:

  • Returns a matrix of environment scores -- test: unit_tests.R#L196
  • Returns a matrix of single cell scores -- test: unit_tests.R#L197

Specs for cellTypeAttribution:

  • Returns a matrix of cell type x module attribution scores -- test: unit_tests.R#L176,177,178,179
  • Returns a list of cell type x gene attribution scores -- test: unit_tests.R#L180,181,182,182

Specs for plotCorrelationNetwork

  • Draws a plot -- test: unit_tests.R#L189,190