Merge pull request #72 from NIDAP-Community/dev

Dev

Author: escauley

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: DSPWorkflow
 Title: A Workflow for Analyzing Digital Spatial Profiling RNA Data
-Version: 0.9.2.0
+Version: 0.9.4.0
 Authors@R: c(person("Rui", "He", email = "[email protected]", role = "aut"), 
     person("Maggie", "Cam", email = "[email protected]", role = "aut", comment = c(ORCID = "0000-0001-8190-9766")), 
     person("Ned", "Cauley", email = "[email protected]", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-8968-6621")), 
@@ -45,7 +45,6 @@ Imports:
     tibble (>= 3.1.8),
     tidyr (>= 1.2.1),
     umap (>= 0.2.9.0),
-    pheatmap (>= 1.0.12),
     magrittr (>= 2.0.3),
     ComplexHeatmap (>= 2.10.0)
 Config/testthat/edition: 3

R/heatmap.R

@@ -95,14 +95,12 @@ heatMap <- function(
                    base = 2,
                    elt = elt.value)
 
-  ## MC: for cv function, use .calcCV - "." means it is a private function and use lowerCamelCase ====
-  
   # create CV function
-  calc.cv <- function(x) {
+  .calcCv <- function(x) {
     sd(x) / mean(x)
   }
   cv.dat <- assayDataApply(object,
-                           elt = "log_q", MARGIN = 1, calc.cv)
+                           elt = "log_q", MARGIN = 1, .calcCv)
   # show the highest CD genes and their CV values
   sort(cv.dat, decreasing = TRUE)[1:5]
 

R/spatial_deconvolution.R

@@ -31,6 +31,7 @@
 #' @importFrom SpatialDecon spatialdecon
 #' @importFrom SpatialDecon create_profile_matrix
 #' @importFrom reshape2 melt
+#' @importFrom ComplexHeatmap pheatmap
 #'
 #' @export
 #' @example Do not run: spatialDeconvolution(object = NanostringGeomx,