Correction following a check()

NAMESPACE

@@ -10,6 +10,7 @@ export(TCGA_expression)
 export(TCGA_methylation_expression_correlation)
 export(all_genes)
 export(embryo_expression)
+export(embryos_mean_methylation)
 export(fetal_germcell_mean_methylation)
 export(fetal_germcells_expression)
 export(hESC_expression)
@@ -58,6 +59,7 @@ importFrom(ggplot2,ylim)
 importFrom(ggrepel,geom_text_repel)
 importFrom(grDevices,colorRampPalette)
 importFrom(grid,gpar)
+importFrom(grid,unit)
 importFrom(rlang,.data)
 importFrom(stats,cor.test)
 importFrom(stats,na.omit)

R/embryo_expression.R

@@ -8,6 +8,9 @@
 #' Petropoulos et al., Cell 2016) or from "Zhu" scRNAseq dataset ("Single-cell 
 #' DNA methylome sequencing of human preimplantation embryos". Zhu et al. 
 #' Nat genetics 2018)
+#' 
+#' @param dataset `character`. Indicates which scRNAseq dataset to use.
+#' Either Petropoulos or Zhu, no default. 
 #'
 #' @param genes `character` nameing the selected genes. The default
 #'     value, `NULL`, takes all CT (specific) genes.

R/embryos_mean_methylation.R

@@ -10,7 +10,7 @@
 #' @param genes `character` naming the selected genes. The default
 #'     value, `NULL`, takes all CT (specific) genes.
 #'     
-#' @param cells `character` defining the cell types to be plotted.
+#' @param stage `character` defining the cell types to be plotted.
 #' Can be "GV Oocyte", "MII Oocyte", "Sperm", "Zygote", "2-cell", 
 #' "4-cell", "8-cell", "Morula", "Blastocyst", "Post-implantation".
 #'     
@@ -28,15 +28,15 @@
 #' @export
 #'
 #' @importFrom ComplexHeatmap Heatmap
-#' @importFrom grid gpar
+#' @importFrom grid gpar unit
 #' @importFrom circlize colorRamp2
 #' @importFrom grDevices colorRampPalette
 #' @importFrom SummarizedExperiment rowData<- assay
 #' 
 #'
 #' @examples
 #' embryos_mean_methylation()
-#' embryos_mean_methylation(c("MAGEA1", "MAGEA3", "MAGEA4", "MAGEC2", "MAGEB16),
+#' embryos_mean_methylation(c("MAGEA1", "MAGEA3", "MAGEA4", "MAGEC2", "MAGEB16"),
 #' stage = c( "MII Oocyte", "Sperm", "Zygote", "2-cell", "4-cell", "8-cell", 
 #' "Morula"))
 embryos_mean_methylation <- function(genes = NULL, 

R/fetal_germcells_mean_methylation.R

@@ -24,7 +24,7 @@
 #' @export
 #'
 #' @importFrom ComplexHeatmap Heatmap
-#' @importFrom grid gpar
+#' @importFrom grid gpar unit
 #' @importFrom circlize colorRamp2
 #' @importFrom grDevices colorRampPalette
 #' @importFrom stats na.omit

R/hESC_mean_methylation.R

@@ -53,7 +53,6 @@ hESC_mean_methylation <- function(genes = NULL,
                col = colorRamp2(seq_len(100),
                                 colorRampPalette(c("moccasin", "dodgerblue4"))(100)),
                na_col = "gray80",
-               cluster_rows = clustering_option,
                cluster_columns = FALSE,
                show_row_names = TRUE,
                show_heatmap_legend = TRUE,