Apply "84 and #86 to vpath year level2

NAMESPACE

@@ -41,7 +41,6 @@ importFrom(dplyr,filter)
 importFrom(dplyr,filter_at)
 importFrom(dplyr,full_join)
 importFrom(dplyr,group_by)
-importFrom(dplyr,if_else)
 importFrom(dplyr,inner_join)
 importFrom(dplyr,left_join)
 importFrom(dplyr,mutate)
@@ -61,10 +60,8 @@ importFrom(dplyr,tally)
 importFrom(dplyr,tibble)
 importFrom(dplyr,ungroup)
 importFrom(dplyr,vars)
-importFrom(egg,ggarrange)
 importFrom(ggplot2,aes)
 importFrom(ggplot2,element_text)
-importFrom(ggplot2,facet_wrap)
 importFrom(ggplot2,geom_bar)
 importFrom(ggplot2,geom_line)
 importFrom(ggplot2,geom_point)
@@ -77,7 +74,6 @@ importFrom(ggplot2,scale_y_continuous)
 importFrom(ggplot2,theme)
 importFrom(ggplot2,xlab)
 importFrom(ggplot2,ylab)
-importFrom(ggplot2,ylim)
 importFrom(grDevices,grey)
 importFrom(graphics,legend)
 importFrom(gratia,derivatives)
@@ -143,7 +139,6 @@ importFrom(stringr,str_to_lower)
 importFrom(svDialogs,dlgInput)
 importFrom(tibble,as_tibble)
 importFrom(tibble,tibble)
-importFrom(tidyselect,all_of)
 importFrom(tidyselect,ends_with)
 importFrom(tidyselect,one_of)
 importFrom(tidyselect,vars_pull)

R/visualize_pathways_level1.R

@@ -141,6 +141,7 @@ visualize_pathways_level1 <- function(df,
         "."
       )
     )
+    assertthat::assert_that(length(category) == 1)
     assertthat::assert_that(category %in% categories,
       msg = paste0(
         "`category` is not correct. Choose one of: ",

R/visualize_pathways_level2.R

@@ -176,21 +176,18 @@ visualize_pathways_level2 <- function(df,
   assertable::assert_colnames(df, pathway_level2_names, only_colnames = FALSE)
   # Check category
   if (!is.null(category)) {
-    valid_categories <- c("Chordata", "Not Chordata", "Plantae", "Animalia",
-                          "Fungi", "Chromista", "Archaea", "Bacteria",
-                          "Protozoa", "Viruses", "incertae sedis")
     assertthat::assert_that(is.character(category),
       msg = paste0(
         "`category` must be NULL or a character. One of: ",
-        paste(valid_categories, collapse = ", "),
+        paste(categories, collapse = ", "),
         "."
       )
     )
     assertthat::assert_that(length(category) == 1)
-    assertthat::assert_that(category %in% valid_categories,
+    assertthat::assert_that(category %in% categories,
       msg = paste0(
         "`category` is not correct. Choose one of: ",
-        paste0(valid_categories, collapse = ", "),
+        paste0(categories, collapse = ", "),
         "."
       )
     )

R/visualize_pathways_year_level1.R

@@ -49,7 +49,7 @@
 #' @param x_lab `NULL` or character. x-axis label. Default: `"Number of
 #'   introduced taxa"`.
 #' @param y_lab `NULL` or character. Title of the graph. Default: `"Pathways"`.
-#' #' @return A list with three slots:
+#' @return A list with three slots:
 #' - `plot`: ggplot2 object (or egg object if facets are used). `NULL` if there
 #' are no data to plot.
 #' - `data_top_graph`: data.frame (tibble) with data used for the main plot (top