@@ -24,10 +24,10 @@ export(featureModuleLookup)

 export(featureModuleTable)

 export(geneSetEnrich)

 export(logLikelihood)

-export(logLikelihood.celda_C)

-export(logLikelihood.celda_CG)

-export(logLikelihood.celda_G)

 export(logLikelihoodHistory)

+export(logLikelihoodcelda_C)

+export(logLikelihoodcelda_CG)

+export(logLikelihoodcelda_G)

 export(matrixNames)

 export(moduleHeatmap)

 export(normalizeCounts)

@@ -38,9 +38,9 @@ export(plotDimReduceFeature)

 export(plotDimReduceGrid)

 export(plotDimReduceModule)

 export(plotGridSearchPerplexity)

-export(plotGridSearchPerplexity.celda_C)

-export(plotGridSearchPerplexity.celda_CG)

-export(plotGridSearchPerplexity.celda_G)

+export(plotGridSearchPerplexitycelda_C)

+export(plotGridSearchPerplexitycelda_CG)

+export(plotGridSearchPerplexitycelda_G)

 export(plotHeatmap)

 export(recodeClusterY)

 export(recodeClusterZ)

@@ -53,9 +53,9 @@ export(sampleLabel)

 export(selectBestModel)

 export(semiPheatmap)

 export(simulateCells)

-export(simulateCells.celda_C)

-export(simulateCells.celda_CG)

-export(simulateCells.celda_G)

+export(simulateCellscelda_C)

+export(simulateCellscelda_CG)

+export(simulateCellscelda_G)

 export(simulateContaminatedMatrix)

 export(subsetCeldaList)

 export(topRank)

@@ -77,22 +77,40 @@ exportMethods(perplexity)

 exportMethods(resList)

 exportMethods(runParams)

 exportMethods(sampleLabel)

-import(MAST, except = c(combine))

-import(RColorBrewer)

 import(Rcpp)

 import(RcppEigen)

-import(SummarizedExperiment, except = c(shift, rowRanges))

-import(data.table)

 import(foreach)

+import(ggplot2)

 import(grDevices)

 import(graphics)

 import(grid)

-import(gridExtra)

-import(gridExtra, except = c(combine))

 import(gtable)

-import(matrixStats, except = c(count))

-import(plyr)

-import(scales)

+import(stats)

+import(umap)

+importFrom(MAST,FromMatrix)

+importFrom(MAST,summary)

+importFrom(MAST,zlm)

+importFrom(MCMCprecision,fit_dirichlet)

+importFrom(RColorBrewer,brewer.pal)

+importFrom(Rtsne,Rtsne)

+importFrom(S4Vectors,mcols)

+importFrom(SummarizedExperiment,assay)

+importFrom(SummarizedExperiment,assayNames)

+importFrom(SummarizedExperiment,colData)

+importFrom(data.table,as.data.table)

+importFrom(digest,digest)

+importFrom(doParallel,registerDoParallel)

+importFrom(enrichR,enrichr)

+importFrom(ggrepel,geom_text_repel)

+importFrom(gridExtra,grid.arrange)

+importFrom(matrixStats,logSumExp)

+importFrom(methods,.hasSlot)

+importFrom(methods,is)

+importFrom(methods,new)

+importFrom(plyr,mapvalues)

+importFrom(reshape2,melt)

+importFrom(scales,dscale)

+importFrom(stringi,stri_list2matrix)

 useDynLib(celda,"_colSumByGroup")

 useDynLib(celda,"_colSumByGroupChange")

 useDynLib(celda,"_colSumByGroup_numeric")

@@ -23,7 +23,6 @@

 #'  p-value, log2 fold change, and FDR.

 #' @examples

 #' data(celdaCGSim, celdaCGMod)

-#' library(SummarizedExperiment)

 #' clusterDiffexpRes = differentialExpression(celdaCGSim$counts,

 #'     celdaCGMod, c1 = c(1, 2))

 #' @export

@@ -23,6 +23,7 @@

 #' gse <- geneSetEnrich(counts,

 #'     cm,

 #'     databases = c('GO_Biological_Process_2018','GO_Molecular_Function_2018'))

+#' @importFrom enrichR enrichr

 #' @export

 geneSetEnrich <- function(counts, celdaModel, databases, fdr = 0.05) {

     #check for correct celda object

similarity index 88%

rename from man/logLikelihood.celda_C.Rd

rename to man/logLikelihoodcelda_C.Rd

@@ -1,10 +1,10 @@

 % Generated by roxygen2: do not edit by hand

 % Please edit documentation in R/celda_C.R

-\name{logLikelihood.celda_C}

-\alias{logLikelihood.celda_C}

+\name{logLikelihoodcelda_C}

+\alias{logLikelihoodcelda_C}

 \title{Calculate Celda_C log likelihood}

 \usage{

-logLikelihood.celda_C(counts, sampleLabel, z, K, alpha, beta)

+logLikelihoodcelda_C(counts, sampleLabel, z, K, alpha, beta)

 }

 \arguments{

 \item{counts}{Integer matrix. Rows represent features and columns represent

@@ -34,7 +34,7 @@ Calculates the log likelihood for user-provided cell population

 }

 \examples{

 data(celdaCSim)

-loglik <- logLikelihood.celda_C(celdaCSim$counts,

+loglik <- logLikelihoodcelda_C(celdaCSim$counts,

     sampleLabel = celdaCSim$sampleLabel,

     z = celdaCSim$z,

     K = celdaCSim$K,

similarity index 91%

rename from man/logLikelihood.celda_CG.Rd

rename to man/logLikelihoodcelda_CG.Rd

@@ -1,10 +1,10 @@

 % Generated by roxygen2: do not edit by hand

 % Please edit documentation in R/celda_CG.R

-\name{logLikelihood.celda_CG}

-\alias{logLikelihood.celda_CG}

+\name{logLikelihoodcelda_CG}

+\alias{logLikelihoodcelda_CG}

 \title{Calculate Celda_CG log likelihood}

 \usage{

-logLikelihood.celda_CG(counts, sampleLabel, z, y, K, L, alpha, beta, delta,

+logLikelihoodcelda_CG(counts, sampleLabel, z, y, K, L, alpha, beta, delta,

   gamma)

 }

 \arguments{

@@ -45,7 +45,7 @@ Calculates the log likelihood for user-provided cell population

 }

 \examples{

 data(celdaCGSim)

-loglik <- logLikelihood.celda_CG(celdaCGSim$counts,

+loglik <- logLikelihoodcelda_CG(celdaCGSim$counts,

     sampleLabel = celdaCGSim$sampleLabel,

     z = celdaCGSim$z,

     y = celdaCGSim$y,

similarity index 89%

rename from man/logLikelihood.celda_G.Rd

rename to man/logLikelihoodcelda_G.Rd

@@ -1,10 +1,10 @@

 % Generated by roxygen2: do not edit by hand

 % Please edit documentation in R/celda_G.R

-\name{logLikelihood.celda_G}

-\alias{logLikelihood.celda_G}

+\name{logLikelihoodcelda_G}

+\alias{logLikelihoodcelda_G}

 \title{Calculate Celda_G log likelihood}

 \usage{

-logLikelihood.celda_G(counts, y, L, beta, delta, gamma)

+logLikelihoodcelda_G(counts, y, L, beta, delta, gamma)

 }

 \arguments{

 \item{counts}{Integer matrix. Rows represent features and columns represent

@@ -34,7 +34,7 @@ Calculates the log likelihood for user-provided feature module

 }

 \examples{

 data(celdaGSim)

-loglik <- logLikelihood.celda_G(celdaGSim$counts,

+loglik <- logLikelihoodcelda_G(celdaGSim$counts,

     y = celdaGSim$y,

     L = celdaGSim$L,

     beta = celdaGSim$beta,

similarity index 84%

rename from man/plotGridSearchPerplexity.celda_C.Rd

rename to man/plotGridSearchPerplexitycelda_C.Rd

@@ -1,10 +1,10 @@

 % Generated by roxygen2: do not edit by hand

 % Please edit documentation in R/model_performance.R

-\name{plotGridSearchPerplexity.celda_C}

-\alias{plotGridSearchPerplexity.celda_C}

+\name{plotGridSearchPerplexitycelda_C}

+\alias{plotGridSearchPerplexitycelda_C}

 \title{Plot perplexity as a function of K from celda_C models}

 \usage{

-plotGridSearchPerplexity.celda_C(celdaList, sep)

+plotGridSearchPerplexitycelda_C(celdaList, sep)

 }

 \arguments{

 \item{celdaList}{Object of class 'celdaList'.}

similarity index 84%

rename from man/plotGridSearchPerplexity.celda_CG.Rd

rename to man/plotGridSearchPerplexitycelda_CG.Rd

@@ -1,10 +1,10 @@

 % Generated by roxygen2: do not edit by hand

 % Please edit documentation in R/model_performance.R

-\name{plotGridSearchPerplexity.celda_CG}

-\alias{plotGridSearchPerplexity.celda_CG}

+\name{plotGridSearchPerplexitycelda_CG}

+\alias{plotGridSearchPerplexitycelda_CG}

 \title{Plot perplexity as a function of K and L from celda_CG models}

 \usage{

-plotGridSearchPerplexity.celda_CG(celdaList, sep)

+plotGridSearchPerplexitycelda_CG(celdaList, sep)

 }

 \arguments{

 \item{celdaList}{Object of class 'celdaList'.}

similarity index 84%

rename from man/plotGridSearchPerplexity.celda_G.Rd

rename to man/plotGridSearchPerplexitycelda_G.Rd

@@ -1,10 +1,10 @@

 % Generated by roxygen2: do not edit by hand

 % Please edit documentation in R/model_performance.R

-\name{plotGridSearchPerplexity.celda_G}

-\alias{plotGridSearchPerplexity.celda_G}

+\name{plotGridSearchPerplexitycelda_G}

+\alias{plotGridSearchPerplexitycelda_G}

 \title{Plot perplexity as a function of L from a celda_G model}

 \usage{

-plotGridSearchPerplexity.celda_G(celdaList, sep)

+plotGridSearchPerplexitycelda_G(celdaList, sep)

 }

 \arguments{

 \item{celdaList}{Object of class 'celdaList'.}

similarity index 93%

rename from man/simulateCells.celda_C.Rd

rename to man/simulateCellscelda_C.Rd

@@ -1,10 +1,10 @@

 % Generated by roxygen2: do not edit by hand

 % Please edit documentation in R/celda_C.R

-\name{simulateCells.celda_C}

-\alias{simulateCells.celda_C}

+\name{simulateCellscelda_C}

+\alias{simulateCellscelda_C}

 \title{Simulate cells from the celda_C model}

 \usage{

-simulateCells.celda_C(model, S = 5, CRange = c(50, 100),

+simulateCellscelda_C(model, S = 5, CRange = c(50, 100),

   NRange = c(500, 1000), G = 100, K = 5, alpha = 1, beta = 1,

   ...)

 }

similarity index 94%

rename from man/simulateCells.celda_CG.Rd

rename to man/simulateCellscelda_CG.Rd

@@ -1,10 +1,10 @@

 % Generated by roxygen2: do not edit by hand

 % Please edit documentation in R/celda_CG.R

-\name{simulateCells.celda_CG}

-\alias{simulateCells.celda_CG}

+\name{simulateCellscelda_CG}

+\alias{simulateCellscelda_CG}

 \title{Simulate cells from the celda_CG model}

 \usage{

-simulateCells.celda_CG(model, S = 5, CRange = c(50, 100),

+simulateCellscelda_CG(model, S = 5, CRange = c(50, 100),

   NRange = c(500, 1000), G = 100, K = 5, L = 10, alpha = 1,

   beta = 1, gamma = 5, delta = 1, ...)

 }

similarity index 92%

rename from man/simulateCells.celda_G.Rd

rename to man/simulateCellscelda_G.Rd

@@ -1,10 +1,10 @@

 % Generated by roxygen2: do not edit by hand

 % Please edit documentation in R/celda_G.R

-\name{simulateCells.celda_G}

-\alias{simulateCells.celda_G}

+\name{simulateCellscelda_G}

+\alias{simulateCellscelda_G}

 \title{Simulate cells from the celda_G model}

 \usage{

-simulateCells.celda_G(model, C = 100, NRange = c(500, 1000), G = 100,

+simulateCellscelda_G(model, C = 100, NRange = c(500, 1000), G = 100,

   L = 10, beta = 1, gamma = 5, delta = 1, ...)

 }

 \arguments{

deleted file mode 100644

@@ -1,54 +0,0 @@

-library(celda)

-context("Testing recursiveSplits")

-

-# celdaCGSim <- simulateCells("celda_CG", K = 5, L = 10)

-#

-# test_that(desc = "Testing recursiveSplitModule", {

-#     moduleSplit <- recursiveSplitModule(

-#         celdaCGSim$counts,

-#         initialL = 8,

-#         maxL = 15,

-#         tempK = 5,

-#         zInit = NULL)

-#     expect_true(is(moduleSplit, "celdaList"))

-#     moduleSplit <- recursiveSplitModule(

-#         celdaCGSim$counts,

-#         initialL = 8,

-#         maxL = 15,

-#         tempK = NULL,

-#         zInit = celdaCGSim$z)

-#     expect_true(is(moduleSplit, "celdaList"))

-#     moduleSplit <- recursiveSplitModule(

-#         celdaCGSim$counts,

-#         initialL = 8,

-#         maxL = 15,

-#         tempK = NULL,

-#         zInit = NULL)

-#     expect_true(is(moduleSplit, "celdaList"))

-#     plotGridSearchPerplexity(moduleSplit)

-# })

-#

-# test_that(desc = "Testing recursiveSplitCell", {

-#     cellSplit <- recursiveSplitCell(

-#         celdaCGSim$counts,

-#         initialK = 3,

-#         maxK = 8,

-#         tempL = 20,

-#         yInit = NULL)

-#     expect_true(is(cellSplit, "celdaList"))

-#     cellSplit <- recursiveSplitCell(

-#         celdaCGSim$counts,

-#         initialK = 3,

-#         maxK = 8,

-#         tempL = NULL,

-#         yInit = celdaCGSim$y)

-#     expect_true(is(cellSplit, "celdaList"))

-#     cellSplit <- recursiveSplitCell(

-#         celdaCGSim$counts,

-#         initialK = 3,

-#         maxK = 8,

-#         tempL = NULL,

-#         yInit = NULL)

-#     expect_true(is(cellSplit, "celdaList"))

-#     plotGridSearchPerplexity(cellSplit)

-# })