more steps to finish qsip_sample_object creation

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: qSIP2
 Title: qSIP Analysis
-Version: 0.4.1.9003
+Version: 0.4.1.9005
 Authors@R: 
     person("Jeff", "Kimbrel", , "[email protected]", role = c("aut", "cre"),
            comment = c(ORCID = "YOUR-ORCID-ID"))

R/qsip_sample_object.R

@@ -48,21 +48,35 @@ qsip_sample_object <- S7::new_class(
 
 plot_sample_curves <- S7::new_generic("plot_sample_curves", "x")
 
-S7::method(plot_sample_curves, qsip_sample_object) <- function(x) {
+S7::method(plot_sample_curves, qsip_sample_object) <- function(x, colors = NULL) {
+
+  if (is.null(colors)) {
+    colors = c("12C" = "lightblue",
+      "13C" = "blue",
+      "14N" = "lightblue",
+      "15N" = "blue",
+      "16O" = "lightblue",
+      "18O" = "blue")
+  }
+
   facet_formula = paste0("~", x@source_mat_id)
 
+  WAD = x@data %>%
+    dplyr::group_by(source_mat_id) %>%
+    dplyr::summarise(WAD = weighted.mean(density_g_ml, gradient_pos_rel_amt))
+
   x@data |>
     dplyr::filter(!is.na(!!as.name(x@gradient_position))) |>
     dplyr::filter(!!as.name(x@gradient_pos_density) > 1.5) |>
     dplyr::group_by(!!as.name(x@source_mat_id)) |>
-    #dplyr::mutate(j = !!as.name(x@gradient_pos_amt) / sum(!!as.name(x@gradient_pos_amt))) |>
     ggplot2::ggplot(ggplot2::aes(x = !!as.name(x@gradient_pos_density),
                                  y = !!as.name(x@gradient_pos_rel_amt),
                                  color = !!as.name(x@isotope))) +
     ggplot2::geom_point() +
     ggplot2::geom_line(linewidth = 1) +
-    ggplot2::scale_color_manual(values = c("16" = "lightblue", "18" = "blue", "16O" = "lightblue", "18O" = "blue", "15" = "yellow")) +
-    ggplot2::facet_wrap(facet_formula, scales = "free")
+    ggplot2::scale_color_manual(values = colors) +
+    ggplot2::facet_wrap(facet_formula) +
+    ggplot2::geom_vline(data = WAD, linetype = 3, ggplot2::aes(xintercept = WAD))
 }
 
 #' Get sample counts from qSIP sample data

R/remove_isotopolog_label.R

@@ -4,15 +4,12 @@
 #'
 #' @param data A dataframe or tibble
 #'
-#' @export
-#'
 #' @keywords sample_data
 #'
 #' @examples
-#' \dontrun{
-#' add_isotopolog_label(sample_data_nonMISIP, isotope = "isotope")
 #' remove_isotopolog_label(sample_data_MISIP)
-#' }
+#'
+#' @export
 
 remove_isotopolog_label = function(data) {
 

R/zzz.R

@@ -0,0 +1,3 @@
+.onLoad <- function(...) {
+  S7::methods_register()
+}