Allow specification which cells are test cells

R/find_de_neighborhoods.R

@@ -516,6 +516,7 @@ neighborhood_count_test <- function(de_regions, counts, group_by, contrast, desi
   }
 
   if(add_diff_in_diff){
+    if(verbose) message("Fit diff-in-diff effect")
     mm <- if(method == "glmGamPoi") glm_regions$model_matrix else glm_regions$design
     mat <- assay(region_psce, "masked_counts")
     complement_mat <- assay(region_psce, "counts") - assay(region_psce, "masked_counts")
@@ -530,7 +531,6 @@ neighborhood_count_test <- function(de_regions, counts, group_by, contrast, desi
     mod_size_factor_matrix <- pseudobulk_size_factors_for_neighborhoods(cbind(counts, counts), mask = cbind(mask, 1-mask),
                                                                         col_data = mod_col_data, group_by = c({{group_by}}, vars(..did_indicator)),
                                                                         method = size_factor_method, verbose = verbose)
-    if(verbose) message("Fit diff-in-diff effect")
     if(method == "glmGamPoi"){
       did_fit <- glmGamPoi::glm_gp(comb_mat, design = comb_design_mat, verbose = FALSE,
                                    offset = log(mod_size_factor_matrix + 1e-10),

R/lemur.R

@@ -17,7 +17,8 @@
 #' @param use_assay if `data` is a `SummarizedExperiment` / `SingleCellExperiment` object,
 #'   which assay should be used.
 #' @param test_fraction the fraction of cells that are split of before the model fit to keep an
-#'   independent set of test observations. Default: 20% (`0.2`).
+#'   independent set of test observations. Alternatively, a logical vector of length `ncol(data)`.
+#'   Default: 20% (`0.2`).
 #' @param ... additional parameters that are passed on to the internal function `lemur_impl`.
 #' @param verbose Should the method print information during the fitting. Default: `TRUE`.
 #'
@@ -61,7 +62,12 @@ lemur <- function(data, design = ~ 1, col_data = NULL,
 
   # Create indicator vector which cells are used for training and which for testing
   is_test_data <- rep(FALSE, ncol(data))
-  if(test_fraction < 0 || test_fraction >= 1){
+  if(is.logical(test_fraction) && length(ncol(data))){
+    if(any(is.na(test_fraction))) stop("test_fraction must not contain 'NA's.")
+    is_test_data <- test_fraction
+  }else if(length(test_fraction) != 1){
+    stop("'test_fraction' must be a boolean vector of length 'ncol(data)' or a single number between 0 and 1.")
+  }else if(test_fraction < 0 || test_fraction >= 1){
     stop("'test_fraction' must be at least 0 and smaller than 1.")
   }else{
     if(verbose) message("Storing ", round(test_fraction, 2) * 100, "% of the data (", round(ncol(data) * test_fraction), " cells)",