v2.1 Update

DESCRIPTION

@@ -5,7 +5,7 @@ Author: Nanxi Guo, Juan Vargas, Douglas Fritz, Revanth Krishna, Fan Zhang (Unive
 Maintainer: Revanth Krishna <[email protected]>
 Correspondance: Fan Zhang <[email protected]>
 Description: Uncover spatially informed shared variations underlying single-cell spatial transcriptomics with STew.
-Date: 2023-08-01
+Date: 2024-01-24
 License: MIT + file LICENSE
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
@@ -16,11 +16,13 @@ Depends:
     R (>= 4.0),
     ggplot2 (>= 3.4),
     tidyverse,
+    dplyr
 Remotes:
     JEFworks-Lab/MERINGUE,
     satijalab/Seurat
 Imports:
     loe (>= 1.1),
+    RSpectra,
     Matrix (>= 1.5.4),
     ggpubr (>= 0.6.0),
     future,
@@ -31,24 +33,24 @@ Imports:
     sctransform,
     MERINGUE,
     Seurat,
-    viridis,
     data.table,
     parallel,
     MASS,
-    princurve,
-    lme4,
-    lmtest,
-    pscl,
-    vcd,
-    ComplexHeatmap,
     gridExtra,
     ggrepel,
     stats,
     methods,
     parameters
 Suggests: knitr,
     rmarkdown,
-    ggpointdensity
+    ggpointdensity,
+    princurve,
+    lme4,
+    lmtest,
+    pscl,
+    vcd,
+    ComplexHeatmap,
+    viridis
 LazyData: true
 LazyDataCompression: xz
 VignetteBuilder: knitr

NAMESPACE

@@ -18,11 +18,11 @@ export(sct)
 export(spatial_adjacency_matrix)
 export(spatial_gradient)
 export(var_genes)
-import(ComplexHeatmap)
 import(MASS)
 import(MERINGUE)
 import(Matrix)
 import(RANN)
+import(RSpectra)
 import(Seurat)
 import(data.table)
 import(future)
@@ -31,16 +31,10 @@ import(ggplot2)
 import(ggpubr)
 import(ggrepel)
 import(gridExtra)
-import(lme4)
-import(lmtest)
 import(loe)
 import(matrixStats)
 import(parallel)
 import(parameters)
-import(princurve)
-import(pscl)
 import(sctransform)
 import(tibble)
 import(tidyverse)
-import(vcd)
-import(viridis)

R/CheckVs.R

@@ -1,6 +1,13 @@
+#' CheckVS
+#'
+#' @param v v
+#' @param x x
+#' @param z z
+#' @param K K
+#'
+#' @import RSpectra
 CheckVs <- function(v,x,z,K){ # If v is NULL, then get v as appropriate.
   ##print(list(v=v, x = x, z = z, K = K))
-  library(RSpectra)
   if(!is.null(v) && !is.matrix(v)) v <- matrix(v,nrow=ncol(z))
   if(!is.null(v) && ncol(v)<K) v <- NULL
   if(!is.null(v) && ncol(v)>K) v <- matrix(v[,1:K],ncol=K)

R/multimodel_count_regression.R

@@ -22,21 +22,14 @@
 #' @export
 #' @import future
 #' future.apply
-#' princurve
 #' tidyverse
 #' data.table
 #' parallel
 #' MASS
-#' lme4
-#' lmtest
 #' future
-#' pscl
-#' vcd
-#' ComplexHeatmap
 #' ggpubr
 #' gridExtra
 #' ggrepel
-#' viridis
 #' parameters
 multimodel_count_regression <- function(outcomes_interest,  # a vector of genes of interest
                                         models,          # a vector of models to use (e.g., "GLM", "ZeroInflated", etc.)