update documentation

NAMESPACE

@@ -129,6 +129,7 @@ importFrom(scales,hue_pal)
 importFrom(stringi,stri_list2matrix)
 importFrom(umap,umap)
 importFrom(umap,umap.defaults)
+importFrom(withr,with_seed)
 useDynLib(celda,"_colSumByGroup")
 useDynLib(celda,"_colSumByGroupChange")
 useDynLib(celda,"_colSumByGroup_numeric")

R/all_generics.R

@@ -601,9 +601,11 @@ setGeneric("celdaTsne",
 #'  for umap. Default 20.
 #' @param modules Integer vector. Determines which features modules to use for
 #'  tSNE. If NULL, all modules will be used. Default NULL.
+#' @param seed Integer. Passed to \link[withr]{with_seed}. For reproducibility,
+#'  a default value of 12345 is used. If NULL, no calls to
+#'  \link[withr]{with_seed} are made.
 #' @param umapConfig An object of class "umapConfig" specifying parameters to
 #'  the UMAP algorithm.
-#' @param ... Additional parameters.
 #' @return Numeric Matrix of dimension `ncol(counts)` x 2, colums representing
 #'  the "X" and "Y" coordinates in the data's t-SNE represetation.
 #' @examples
@@ -619,6 +621,7 @@ setGeneric("celdaUmap",
         minClusterSize = 100,
         initialDims = 20,
         modules = NULL,
+        seed = 12345,
         umapConfig = umap::umap.defaults) {
         standardGeneric("celdaUmap")
     })

R/celda_C.R

@@ -795,7 +795,6 @@ setMethod("factorizeMatrix", signature(celdaMod = "celda_C"),
 #'  to each cell population in each sample. Default 1.
 #' @param beta Numeric. Concentration parameter for Phi. Adds a pseudocount to
 #'  each feature in each cell population. Default 1.
-#' @param ... Additional parameters.
 #' @return Numeric. The log likelihood for the given cluster assignments
 #' @seealso `celda_C()` for clustering cells
 #' @examples
@@ -1141,7 +1140,6 @@ setMethod("celdaTsne", signature(celdaMod = "celda_C"),
 #'  \link[withr]{with_seed} are made.
 #' @param umapConfig An object of class "umap.config" specifying parameters to
 #'  the UMAP algorithm.
-#' @param ... Additional parameters.
 #' @seealso `celda_C()` for clustering cells and `celdaHeatmap()` for displaying
 #'  expression.
 #' @examples

R/celda_CG.R

@@ -986,7 +986,6 @@ setMethod("factorizeMatrix", signature(celdaMod = "celda_CG"),
 #'  each feature in each module. Default 1.
 #' @param gamma Numeric. Concentration parameter for Eta. Adds a pseudocount to
 #'  the number of features in each module. Default 1.
-#' @param ... Additional parameters.
 #' @return The log likelihood for the given cluster assignments
 #' @seealso `celda_CG()` for clustering features and cells
 #' @examples

R/celda_G.R

@@ -758,7 +758,6 @@ setMethod("factorizeMatrix", signature(celdaMod = "celda_G"),
 #'  each feature in each module. Default 1.
 #' @param gamma Numeric. Concentration parameter for Eta. Adds a pseudocount to
 #'  the number of features in each module. Default 1.
-#' @param ... Additional parameters.
 #' @keywords log likelihood
 #' @return The log-likelihood for the given cluster assignments.
 #' @seealso `celda_G()` for clustering features