diff --git a/DESCRIPTION b/DESCRIPTION index 31f70bb..86784dc 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -41,7 +41,7 @@ Imports: BiocParallel, ggcorrplot, magrittr, - Matrix + mlr3verse Suggests: devtools, testthat (>= 2.1.0), diff --git a/R/CellTypist.R b/R/CellTypist.R index 47b51ac..ba4687b 100644 --- a/R/CellTypist.R +++ b/R/CellTypist.R @@ -213,7 +213,7 @@ RunCellTypist <- function(seuratObj, modelName = "Immune_All_Low.pkl", pThreshol # Cell typist expects a single column: tbl <- utils::read.table(geneFile, sep = '\t') - write.table(tbl$V1, file = geneFile, row.names = FALSE, col.names = FALSE) + utils::write.table(tbl$V1, file = geneFile, row.names = FALSE, col.names = FALSE) # Ensure models present: if (updateModels) { diff --git a/R/Classification.R b/R/Classification.R index 6f4bc1c..61f6caf 100644 --- a/R/Classification.R +++ b/R/Classification.R @@ -101,13 +101,13 @@ TrainModel <- function(training_matrix, celltype, hyperparameter_tuning = F, lea learner <- mlr3::lrn("classif.ranger", importance = "permutation", predict_type = "prob") #Define Ranger Hyperparameter Space (RandomBotv2) - tune_ps <- ps( - num.trees = p_int(lower = 10, upper = 2000), - sample.fraction = p_dbl(lower = 0.1, upper = 1), - respect.unordered.factors = p_fct(levels = c("ignore", "order", "partition")), - min.node.size = p_int(lower = 1, upper = 100), - splitrule = p_fct(levels = c("gini", "extratrees")), - num.random.splits = p_int(lower = 1, upper = 100, depends = splitrule == "extratrees") + tune_ps <- mlr3verse::ps( + num.trees = mlr3verse::p_int(lower = 10, upper = 2000), + sample.fraction = mlr3verse::p_dbl(lower = 0.1, upper = 1), + respect.unordered.factors = mlr3verse::p_fct(levels = c("ignore", "order", "partition")), + min.node.size = mlr3verse::p_int(lower = 1, upper = 100), + splitrule = mlr3verse::p_fct(levels = c("gini", "extratrees")), + num.random.splits = mlr3verse::p_int(lower = 1, upper = 100, depends = splitrule == "extratrees") ) } else if (learner == "classif.xgboost"){ #Update task @@ -115,20 +115,20 @@ TrainModel <- function(training_matrix, celltype, hyperparameter_tuning = F, lea #Define learner learner <- mlr3::lrn("classif.xgboost", predict_type = "prob") #Define XGBoost model's Hyperparameter Space (RandomBotv2) - tune_ps <- ps( - booster = p_fct(levels = c("gblinear", "gbtree", "dart")), - nrounds = p_int(lower = 2, upper = 8, trafo = function(x) as.integer(round(exp(x)))), - eta = p_dbl(lower = -4, upper = 0, trafo = function(x) 10^x), - gamma = p_dbl(lower = -5, upper = 1, trafo = function(x) 10^x), - lambda = p_dbl(lower = -4, upper = 3, trafo = function(x) 10^x), - alpha = p_dbl(lower = -4, upper = 3, trafo = function(x) 10^x), - subsample = p_dbl(lower = 0.1, upper = 1), - max_depth = p_int(lower = 1, upper = 15), - min_child_weight = p_dbl(lower = -1, upper = 0, trafo = function(x) 10^x), - colsample_bytree = p_dbl(lower = 0.1, upper = 1), - colsample_bylevel = p_dbl(lower = 0.1, upper = 1), - rate_drop = p_int(lower = 0, upper = 1, depends = booster == 'dart'), - skip_drop = p_int(lower = 0, upper = 1, depends = booster == 'dart') + tune_ps <- mlr3verse::ps( + booster = mlr3verse::p_fct(levels = c("gblinear", "gbtree", "dart")), + nrounds = mlr3verse::p_int(lower = 2, upper = 8, trafo = function(x) as.integer(round(exp(x)))), + eta = mlr3verse::p_dbl(lower = -4, upper = 0, trafo = function(x) 10^x), + gamma = mlr3verse::p_dbl(lower = -5, upper = 1, trafo = function(x) 10^x), + lambda = mlr3verse::p_dbl(lower = -4, upper = 3, trafo = function(x) 10^x), + alpha = mlr3verse::p_dbl(lower = -4, upper = 3, trafo = function(x) 10^x), + subsample = mlr3verse::p_dbl(lower = 0.1, upper = 1), + max_depth = mlr3verse::p_int(lower = 1, upper = 15), + min_child_weight = mlr3verse::p_dbl(lower = -1, upper = 0, trafo = function(x) 10^x), + colsample_bytree = mlr3verse::p_dbl(lower = 0.1, upper = 1), + colsample_bylevel = mlr3verse::p_dbl(lower = 0.1, upper = 1), + rate_drop = mlr3verse::p_int(lower = 0, upper = 1, depends = booster == 'dart'), + skip_drop = mlr3verse::p_int(lower = 0, upper = 1, depends = booster == 'dart') ) } }