Add Venice method

code/method-pars.R

@@ -129,6 +129,11 @@ cosg_pars <- expand_grid(
 ) %>%
   mutate(file_name = paste0(method))
 
+venice_pars <- expand_grid(
+  method = "venice",
+) %>%
+  mutate(file_name = paste0(method))
+
 method_pars_data <- list(
   findMarkers_pars,
   scoreMarkers_pars,
@@ -145,7 +150,8 @@ method_pars_data <- list(
   smash_pars,
   nsforest_pars,
   cepo_pars,
-  cosg_pars
+  cosg_pars,
+  venice_pars
 )
 
 method_pars <- flatten(map(method_pars_data, ~ transpose(.x, .names = .x$file_name)))

code/run-venice.R

+#' Find marker genes using Venice.
+#'
+#' Wraps functions from the Venice package.
+#'
+#' @param sce A SingleCellExperiment object
+#' @param pars parameters passed to the function
+#'
+#' @return A list containing the time of the computation and results of the
+#'  method.
+#'
+run_venice <- function(sce, pars) {
+
+  `%>%` <- dplyr::`%>%`
+
+  times <- system.time({
+
+    n_groups <- length(unique(colLabels(sce)))
+    out <- vector("list", length = n_groups)
+
+    for (j in seq_len(n_groups)) {
+
+      group <- levels(colLabels(sce))[[j]]
+      x <- colLabels(sce) == group
+
+      count_mat <- counts(sce)
+      if (!isS4(count_mat)) {
+        count_mat <- methods::as(count_mat, "sparseMatrix")
+      }
+
+      raw_group_out <- Signac::VeniceMarker(count_mat, x)
+
+      group_out <- raw_group_out %>%
+        tibble::as_tibble() %>%
+        dplyr::rename(
+          gene = Gene.Name,
+          log_fc = Log2.fold.change,
+        ) %>%
+        dplyr::mutate(
+          p_value = 10^Log10.p.value,
+          p_value_adj = 10^Log10.adjusted.p.value
+        ) %>%
+        dplyr::mutate(
+          cluster = group,
+          raw_statistic = log_fc,
+          scaled_statistic = 0
+        ) %>%
+        tibble::as_tibble()
+
+      out[[j]] <- group_out
+    }
+
+    result <- dplyr::bind_rows(!!!out)
+  })
+
+  # Get the elapsed time.
+  time <- times[[3]]
+
+  validate_mgs_result(result)
+
+  list(time = time, result = result, raw_result = result, pars = pars)
+}

smash-fork @ 5d40f5d7

+Subproject commit 5d40f5d799452fcfb69b255989831b9a0ddd4547