remove non-ASCI characters for check

cole-trapnell-lab · Sep 18, 2019 · 8bb2eeb · 8bb2eeb
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Showing 5 changed files with 14 additions and 11 deletions.
diff --git a/R/alignment.R b/R/alignment.R
@@ -14,7 +14,7 @@
 #'
 #' Haghverdi L, Lun ATL, Morgan MD, Marioni JC (2018). "Batch effects in
 #' single-cell RNA-sequencing data are corrected by matching mutual nearest
-#' neighbors." Nat. Biotechnol., 36(5), 421–427. doi: 10.1038/nbt.4091
+#' neighbors." Nat. Biotechnol., 36(5), 421-427. doi: 10.1038/nbt.4091
 #'
 #' @param cds the cell_data_set upon which to perform this operation
 #' @param preprocess_method a string specifying the low-dimensional space
@@ -71,7 +71,7 @@ align_cds <- function(cds,
                   "Morgan MD, Marioni JC (2018). 'Batch effects in",
                   "single-cell RNA-sequencing data are corrected by matching",
                   "mutual nearest neighbors.' Nat. Biotechnol., 36(5),",
-                  "421–427. doi: 10.1038/nbt.4091"))
+                  "421-427. doi: 10.1038/nbt.4091"))
     corrected_PCA = batchelor::fastMNN(as.matrix(preproc_res),
                                        batch=colData(cds)[,alignment_group],
                                        k=alignment_k,

diff --git a/R/cell_data_set.R b/R/cell_data_set.R
@@ -104,7 +104,7 @@ new_cell_data_set <- function(expression_data,
                   "named 'gene_short_name' for certain functions."))
   }
 
-  sce <- SingleCellExperiment(list(counts=as(expression_data, "dgCMatrix")),
+  sce <- SingleCellExperiment(list(counts=methods::as(expression_data, "dgCMatrix")),
                               rowData = gene_metadata,
                               colData = cell_metadata)
 

diff --git a/R/utils.R b/R/utils.R
@@ -730,17 +730,17 @@ clear_cds_slots <- function(cds) {
 add_citation <- function(cds, citation_key) {
   citation_map <- list(
     UMAP = c("UMAP", "McInnes, L., Healy, J. & Melville, J. UMAP: Uniform Manifold Approximation and Projection for dimension reduction. Preprint at https://arxiv.org/abs/1802.03426 (2018)."),
-    MNN_correct = c("MNN Correct", "Haghverdi, L. et. al. Batch effects in single-cell RNA-sequencing data are corrected by matching mutual nearest neighbors. Nat. Biotechnol. 36, 421–427 (2018). https://doi.org/10.1038/nbt.4091"),
-    partitions = c("paritioning", c("Levine, J. H., et. al. Data-driven phenotypic dissection of AML reveals progenitor-like cells that correlate with prognosis. Cell 162, 184–197 (2015). https://doi.org/10.1016/j.cell.2015.05.047",
+    MNN_correct = c("MNN Correct", "Haghverdi, L. et. al. Batch effects in single-cell RNA-sequencing data are corrected by matching mutual nearest neighbors. Nat. Biotechnol. 36, 421-427 (2018). https://doi.org/10.1038/nbt.4091"),
+    partitions = c("paritioning", c("Levine, J. H., et. al. Data-driven phenotypic dissection of AML reveals progenitor-like cells that correlate with prognosis. Cell 162, 184-197 (2015). https://doi.org/10.1016/j.cell.2015.05.047",
                                   "Wolf, F. A. et. al. PAGA: graph abstraction reconciles clustering with trajectory inference through a topology preserving map of single cells. Genome Biol. 20, 59 (2019). https://doi.org/10.1186/s13059-019-1663-x")),
-    clusters = c("clustering", "Levine, J. H. et. al. Data-driven phenotypic dissection of AML reveals progenitor-like cells that correlate with prognosis. Cell 162, 184–197 (2015). https://doi.org/10.1016/j.cell.2015.05.047"),
+    clusters = c("clustering", "Levine, J. H. et. al. Data-driven phenotypic dissection of AML reveals progenitor-like cells that correlate with prognosis. Cell 162, 184-197 (2015). https://doi.org/10.1016/j.cell.2015.05.047"),
     leiden = c("leiden", "Traag, V.A., Waltman, L. & van Eck, N.J. From Louvain to Leiden: guaranteeing well-connected communities. Scientific Reportsvolume 9, Article number: 5233 (2019). https://doi.org/10.1038/s41598-019-41695-z" )
   )
   if (is.null(metadata(cds)$citations) | citation_key == "Monocle") {
     metadata(cds)$citations <- data.frame(method = c("Monocle", "Monocle", "Monocle"),
-                                          citations = c("Trapnell C. et. al. The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells. Nat. Biotechnol. 32, 381–386 (2014). https://doi.org/10.1038/nbt.2859",
-                                                        "Qiu, X. et. al. Reversed graph embedding resolves complex single-cell trajectories. Nat. Methods 14, 979–982 (2017). https://doi.org/10.1038/nmeth.4402",
-                                                        "Cao, J. et. al. The single-cell transcriptional landscape of mammalian organogenesis. Nature 566, 496–502 (2019). https://doi.org/10.1038/s41586-019-0969-x"))
+                                          citations = c("Trapnell C. et. al. The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells. Nat. Biotechnol. 32, 381-386 (2014). https://doi.org/10.1038/nbt.2859",
+                                                        "Qiu, X. et. al. Reversed graph embedding resolves complex single-cell trajectories. Nat. Methods 14, 979-982 (2017). https://doi.org/10.1038/nmeth.4402",
+                                                        "Cao, J. et. al. The single-cell transcriptional landscape of mammalian organogenesis. Nature 566, 496-502 (2019). https://doi.org/10.1038/s41586-019-0969-x"))
   }
   metadata(cds)$citations <- rbind(metadata(cds)$citations,
                                    data.frame(method = citation_map[[citation_key]][1],

diff --git a/inst/WORDLIST b/inst/WORDLIST
@@ -118,7 +118,7 @@ Batchelor
 Biotechnol
 CDSs
 Eck
-Hadhverdi
+Haghverdi
 JC
 Lun
 Marioni
@@ -132,3 +132,6 @@ nbt
 ncenter
 str
 residual_model_formula_str
+MNNCorrect
+pre
+reticulate
diff --git a/man/align_cds.Rd b/man/align_cds.Rd