Conversation
remove decontX vignette to fix timeout
…hanged initialization to use UMAP from scater. Updated docs. Modified DexontX vignette to analyze PBMC4k. Added function to find features in a matrix or SCE object
…it was faster and didn't prodcue warnings when checking
…or more or less estimation of contamination
…ssays side by side
…fault and to do scaling separately. Updated vignettes accordingly
…tX. Modified existing violinplot for celda clusters
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R/celda_C.R:72:40: style: Opening curly braces should never go on their own line and should always be followed by a new line. setGeneric("celda_C", function(x, ...) {standardGeneric("celda_C")})
^R/celda_CG.R:85:41: style: Opening curly braces should never go on their own line and should always be followed by a new line. setGeneric("celda_CG", function(x, ...) {standardGeneric("celda_CG")})
^R/celda_G.R:57:40: style: Opening curly braces should never go on their own line and should always be followed by a new line. setGeneric("celda_G", function(x, ...) {standardGeneric("celda_G")})
^R/celda_G.R:802:1: style: Trailing blank lines are superfluous.
^R/celdaProbabilityMap.R:212:1: style: Trailing blank lines are superfluous.
^R/factorizeMatrix.R:29:32: style: Opening curly braces should never go on their own line and should always be followed by a new line. function(x, celdaMod, ...) {standardGeneric("factorizeMatrix")})
^R/featureModuleLookup.R:17:24: style: Opening curly braces should never go on their own line and should always be followed by a new line. function(sce, ...) {standardGeneric("featureModuleLookup")})
^R/geneSetEnrich.R:26:46: style: Opening curly braces should never go on their own line and should always be followed by a new line. setGeneric("geneSetEnrich", function(x, ...) {standardGeneric("geneSetEnrich")})
^R/loglikelihood.R:38:15: style: Use <-, not =, for assignment. delta = S4Vectors::metadata(x)$celda_parameters$delta
^R/loglikelihood.R:39:15: style: Use <-, not =, for assignment. gamma = S4Vectors::metadata(x)$celda_parameters$gamma
^R/loglikelihood.R:80:11: style: Use <-, not =, for assignment. z = celdaClusters(celdaMod)$z
^R/loglikelihood.R:81:11: style: Use <-, not =, for assignment. K = params(celdaMod)$K
^R/loglikelihood.R:82:15: style: Use <-, not =, for assignment. alpha = params(celdaMod)$alpha
^R/loglikelihood.R:83:14: style: Use <-, not =, for assignment. beta = params(celdaMod)$beta
^R/loglikelihood.R:102:14: style: Use <-, not =, for assignment. beta = params(celdaMod)$beta
^R/loglikelihood.R:103:15: style: Use <-, not =, for assignment. delta = params(celdaMod)$delta
^R/loglikelihood.R:104:15: style: Use <-, not =, for assignment. gamma = params(celdaMod)$gamma
^R/loglikelihood.R:126:15: style: Use <-, not =, for assignment. alpha = params(celdaMod)$alpha
^R/loglikelihood.R:127:14: style: Use <-, not =, for assignment. beta = params(celdaMod)$beta
^R/loglikelihood.R:128:15: style: Use <-, not =, for assignment. delta = params(celdaMod)$delta
^R/loglikelihood.R:129:15: style: Use <-, not =, for assignment. gamma = params(celdaMod)$gamma
^R/perplexity.R:25:32: style: Opening curly braces should never go on their own line and should always be followed by a new line. function(x, celdaMod, ...) {standardGeneric("perplexity")})
^R/StateHeatmap.R:44:46: style: Opening curly braces should never go on their own line and should always be followed by a new line. setGeneric("moduleHeatmap", function(x, ...) {standardGeneric("moduleHeatmap")})
^tests/testthat/test-celda_C.R:340:1: style: Lines should not be more than 80 characters. # test_that(desc = "Testing celdaTsne with celda_C including a subset of cells", {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~tests/testthat/test-celda_C.R:378:1: style: Lines should not be more than 80 characters. # test_that(desc = "Testing celdaUmap with celda_C including a subset of cells", {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~tests/testthat/test-celda_G.R:363:1: style: Lines should not be more than 80 characters. # test_that(desc = "Testing celdaTsne with celda_G including a subset of cells", {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~tests/testthat/test-celda_G.R:402:1: style: Lines should not be more than 80 characters. # test_that(desc = "Testing celdaUmap with celda_G including a subset of cells", {
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ |
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R/celdaProbabilityMap.R:212:1: style: Trailing blank lines are superfluous.
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R/celdaGridSearch.R:676:33: style: Remove spaces before the left parenthesis in a function call. .subsetCeldaListSCE <- function (x, ix) {
^R/model_performance.R:649:1: style: Trailing blank lines are superfluous.
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R/celdaGridSearch.R:676:33: style: Remove spaces before the left parenthesis in a function call. .subsetCeldaListSCE <- function (x, ix) {
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4 participants
celda_C,celda_G, andcelda_CGnow returns aSingleCellExperimentobject which can be passed to downstream celda functions.