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devtools::check passed
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nfancy committed Feb 18, 2024
1 parent 73b9551 commit ec7cc06
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1 change: 0 additions & 1 deletion DESCRIPTION
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Expand Up @@ -75,7 +75,6 @@ Imports:
limma (>= 3.54.0),
magrittr (>= 2.0.3),
MAST (>= 1.24.0),
lme4,
methods,
monocle3 (>= 1.3.1),
paletteer (>= 1.5.0),
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13 changes: 10 additions & 3 deletions R/cluster_sce.R
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Expand Up @@ -7,10 +7,17 @@
#' UMAP_Liger, tSNE_Liger.
#' @param resolution Clustering resolution. If NULL, clustering method will be
#' set to louvain.
#' @param K Integer number of nearest neighbors to use when creating the k
#' @param k Integer number of nearest neighbors to use when creating the k
#' nearest neighbor graph for Louvain/Leiden clustering.
#' k is related to the resolution of the clustering result, a bigger k will
#' result in lower resolution and vice versa. Default is 50.
#' @param louvain_iter Integer number of iterations used for Louvain clustering.
#' The clustering result giving the largest modularity score will be used
#' as the final clustering result. Default is 1. Note that if num_iter
#' is greater than 1, the random_seed argument will be ignored
#' for the louvain method.
#' @param verbose A logic flag to determine whether or not we should print
#' the run details.
#' @param ... see monocle3::cluster_cells for more clustering options.
#'
#' @return sce a SingleCellExperiment object annotated with reducedDims
Expand All @@ -23,9 +30,9 @@
#' @export

cluster_sce <- function(sce,
cluster_method = "leiden",
cluster_method = "louvain",
reduction_method = "UMAP_Liger",
resolution = 1e-5,
resolution = NULL,
k = 50,
louvain_iter = 1,
verbose = T,
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4 changes: 2 additions & 2 deletions R/map_with_ewce.R
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Expand Up @@ -263,9 +263,9 @@ map_celltypes_sce <- function(sce,
### Allow variation in annotation level

.map_celltypes <- function(ctdToMap,
ctdToMapAgainst = MAGMA.Celltyping::ctd_Tasic,
ctdToMapAgainst,
inputSpecies = "human",
mapAgainstSpecies = "mouse",
mapAgainstSpecies = "human",
annotLevel = 1,
numTopMarkers = 50,
mappingLevel = 2,
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19 changes: 14 additions & 5 deletions man/cluster_sce.Rd

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4 changes: 2 additions & 2 deletions man/dot-map_celltypes.Rd

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