some fixes

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: qSIP2
 Title: qSIP Analysis
-Version: 0.3.3
+Version: 0.3.4
 Authors@R: 
     person("Jeff", "Kimbrel", , "[email protected]", role = c("aut", "cre"),
            comment = c(ORCID = "YOUR-ORCID-ID"))

NAMESPACE

@@ -1,5 +1,6 @@
 # Generated by roxygen2: do not edit by hand
 
+export(get_sample_counts)
 export(gradient_pos_density_validation)
 export(gradient_position_validation)
 export(isotope_validation)

R/qsip_sample_object.R

@@ -31,3 +31,48 @@ qsip_sample_object <- S7::new_class("qsip_sample_object",
                                   qSIP2::gradient_position_validation(self@data %>% pull(self@gradient_position))
                                 }
 )
+
+
+
+
+
+
+#' Plot qSIP sample data density curves
+#'
+#' @param x An object of `qsip_sample_object` class
+#'
+#' @export
+#'
+
+plot_sample_curves <- S7::new_generic("plot_sample_curves", "x")
+
+S7::method(plot_sample_curves, qsip_sample_object) <- function(x) {
+  facet_formula = paste0("~", x@source_mat_id)
+
+  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(aes(x = !!as.name(x@gradient_pos_density), y = j)) +
+    ggplot2::geom_point(aes(color = !!as.name(x@isotope))) +
+    ggplot2::geom_line(aes(color = !!as.name(x@isotope)), 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")
+
+}
+
+#' Get sample counts from qSIP sample data
+#'
+#' @param x An object of `qsip_sample_object` class
+#'
+#' @export
+#'
+
+get_sample_counts <- S7::new_generic("get_sample_counts", "x")
+
+S7::method(get_sample_counts, qsip_sample_object) <- function(x) {
+  x@data[x@source_mat_id] |>
+    dplyr::rename(source_mat_id = x@source_mat_id) |>
+    dplyr::count(source_mat_id)
+}