diff --git a/DESCRIPTION b/DESCRIPTION index 9ad1942..df57bc2 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Package: monocle3 Title: Clustering, Differential Expression, and Trajectory Analysis for Single-Cell RNA-Seq -Version: 1.3.4 +Version: 1.3.5 Authors@R: c( person(given = "Hannah", family = "Pliner", @@ -96,6 +96,7 @@ Imports: RcppHNSW (>= 0.3.0), Rtsne (>= 0.15), S4Vectors, + sf, shiny, slam (>= 0.1-45), spdep (>= 1.1-2), @@ -105,7 +106,6 @@ Imports: SummarizedExperiment (>= 1.11.5), utils, uwot (>= 0.1.8), - terra (>= 1.4-17), tibble (>= 2.1.1), tidyr (>= 0.8.3), viridis (>= 0.5.1) diff --git a/NAMESPACE b/NAMESPACE index 521aae5..b36dc6f 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -107,6 +107,5 @@ importFrom(future,value) importFrom(igraph,dfs) importFrom(lme4,glmer) importFrom(plyr,".") -importFrom(terra,gdal) importFrom(utils,packageVersion) useDynLib(monocle3, .registration = TRUE) diff --git a/R/expr_models.R b/R/expr_models.R index 53788ad..93aa585 100644 --- a/R/expr_models.R +++ b/R/expr_models.R @@ -432,6 +432,9 @@ extract_coefficient_helper = function(model, model_summary, # We need this because some summary methods "format" the coefficients into # a factor... coef_mat <- apply(coef_mat, 2, function(x) {as.numeric(as.character(x)) }) + if (!is.matrix(coef_mat)) { + coef_mat = t(as.matrix(coef_mat)) + } row.names(coef_mat) = row.names(model_summary$coefficients) colnames(coef_mat) = c('estimate', 'std_err', diff --git a/R/graph_test.R b/R/graph_test.R index 1cfe46c..0aadf7f 100644 --- a/R/graph_test.R +++ b/R/graph_test.R @@ -104,8 +104,6 @@ #' pr_graph_test_res <- graph_test(cds, neighbor_graph="knn") #' } #' -#' @importFrom terra gdal -#' #' @export graph_test <- function(cds, neighbor_graph = c("knn", "principal_graph"),