v0.16.15

update vignettes

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: qSIP2
 Title: qSIP Analysis
-Version: 0.16.14
+Version: 0.16.15
 Authors@R: 
     person("Jeff", "Kimbrel", , "[email protected]", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0001-7213-9392"))

NAMESPACE

@@ -41,10 +41,10 @@ export(pivot_kbase_amplicon_matrix)
 export(plot_EAF_values)
 export(plot_density_outliers)
 export(plot_feature_curves)
+export(plot_feature_occurrence)
 export(plot_feature_resamplings)
 export(plot_filter_gradient_position)
 export(plot_growth_values)
-export(plot_resampling_convergence)
 export(plot_sample_curves)
 export(plot_source_wads)
 export(plot_successful_resamples)

NEWS.md

@@ -4,6 +4,7 @@
     * `vignette("growth")`
     * `vignette("multiple_objects")`
     * `vignette("filtering")`
+    * `vignette("EAF")`
 * The previous vignettes were hastily written, but now they have been hastily re-written to capture the modern workflow of `qSIP2`
     * `vignette("qSIP_workflow")`
     * `vignette("source_data")`

R/plot_feature_occurrence.R

@@ -0,0 +1,105 @@
+#' Plot occurrence of features in samples
+#'
+#' This is a plotting function to visualize the occurrence of features in samples.
+#' The function takes a qsip_data object and a vector of feature_ids, and can scale
+#' the results by total abundance or source abundance, and the WAD value can also be shown.
+#'
+#' @param qsip_data_object (*qsip_data*) A qsip_data object
+#' @param feature_ids (*character*) A vector of feature_ids
+#' @param scale (*character*) A character string
+#' @param show_wad (*logical*) A logical value
+#' @param title (*character*) A character string
+#' @param legend.position (*character* or *numeric vector*) Values passed to ggplot2::theme(legend.position = ...)
+#'
+#' @export
+#'
+#' @returns Returns a ggplot object
+
+plot_feature_occurrence = function(qsip_data_object,
+                                   feature_ids,
+                                   scale = "none",
+                                   show_wad = FALSE,
+                                   title = NULL,
+                                   legend.position = "right") {
+
+  # stop if qsip_data_object !is_qsip()
+  if (!is_qsip_data(qsip_data_object)) {
+    stop("Input must be a <qsip_data> object", call. = F)
+  }
+
+  # features must be a vector, and not too big
+  if (!is.vector(feature_ids)) {
+    stop("feature_ids must be a vector", call. = F)
+  } else if (length(feature_ids) > 64) {
+    stop("The length of feature_ids is capped at 64", call. = F)
+  }
+
+  # scale must be "none", "total", or "source"
+  if (!scale %in% c("none", "total", "source")) {
+    stop("scale must be 'none', 'total', or 'source'", call. = F)
+  }
+
+  # show_wad must be boolean
+  if (!is.logical(show_wad)) {
+    stop("show_wad must be a boolean", call. = F)
+  }
+
+  # title must be a character or NULL
+  if (!is.character(title) & !is.null(title)) {
+    stop("title must be a character or NULL", call. = F)
+  }
+
+
+
+  # make dataframe with joined metadata
+  df = qsip_data_object@tube_rel_abundance |>
+    dplyr::filter(feature_id %in% feature_ids) |>
+    dplyr::left_join(qsip_data_object@sample_data@data,
+              by = join_by(sample_id, source_mat_id, gradient_pos_density, gradient_pos_rel_amt)) |>
+    dplyr::left_join(qsip_data_object@source_data@data,
+              by = join_by(source_mat_id)) |>
+    dplyr::left_join(qsip_data_object@wads,
+              by = join_by(feature_id, source_mat_id))
+
+  # if scale = "source"
+  if (scale == "source") {
+    df = df |>
+      dplyr::mutate(tube_rel_abundance_source = tube_rel_abundance / sum(tube_rel_abundance),
+                    .by = c("feature_id", "source_mat_id"))
+  }
+
+  # base plot
+  p = df |>
+    ggplot2::ggplot(ggplot2::aes(y = source_mat_id))
+
+  # if show_wad is true
+  if (isTRUE(show_wad)) {
+    p = p +
+      ggplot2::geom_point(pch = "|", size = 6,
+                          ggplot2::aes(x = WAD, color = isotope)) +
+      ggplot2::scale_color_manual(values = isotope_palette)
+  }
+
+  # choose which size to plot based on scale argument
+  if (scale == "total") {
+    p = p +
+      ggplot2::geom_point(pch = 21, alpha = 0.9,
+                          ggplot2::aes(x = gradient_pos_density, size = tube_rel_abundance, fill = isotope))
+  } else if (scale == "source") {
+    p = p +
+      ggplot2::geom_point(pch = 21, alpha = 0.9,
+                          ggplot2::aes(x = gradient_pos_density, size = tube_rel_abundance_source, fill = isotope))
+  } else {
+    p = p +
+      ggplot2::geom_point(pch = 21, alpha = 0.9, size = 2,
+                          ggplot2::aes(x = gradient_pos_density, fill = isotope))
+  }
+
+
+  # finish and return plot
+  p +
+    ggplot2::facet_wrap(~feature_id) +
+    ggplot2::scale_fill_manual(values = isotope_palette) +
+    ggplot2::labs(title = title) +
+    ggplot2::theme(legend.position = legend.position)
+}

R/plot_feature_resamplings.R

@@ -69,7 +69,8 @@ plot_feature_resamplings <- function(qsip_data_object,
     ggplot2::ggplot(ggplot2::aes(x = mean_resampled_WAD, y = type)) +
     ggplot2::facet_wrap(~feature_id, scales = "free_x") +
     ggplot2::scale_color_manual(values = c("labeled" = "#ff0000", "unlabeled" = "#037bcf")) +
-    ggplot2::scale_fill_manual(values = c("labeled" = "#FF000055", "unlabeled" = "#037bcf55"))
+    ggplot2::scale_fill_manual(values = c("labeled" = "#FF000055", "unlabeled" = "#037bcf55")) +
+    ggplot2::labs(x = "Resampled WAD Values")
 
   if (isTRUE(area)) {
     p <- p +

R/plot_resampling_convergence.R

@@ -1,8 +1,6 @@
 #' Plot resampling convergence (under construction!)
 #'
 #' @param qsip_data_object (*qsip_data*) A qsip data object that has been resampled
-#'
-#' @export
 
 plot_resampling_convergence = function(qsip_data_object) {
 
@@ -27,12 +25,14 @@ plot_resampling_convergence = function(qsip_data_object) {
   )
 
   dplyr::bind_rows(k) |>
-    dplyr:: mutate(L = (mean_resampled_EAF - lower) / mean_resampled_EAF,
-                   U = (mean_resampled_EAF - upper) / mean_resampled_EAF) |>
-    tidyr::pivot_longer(cols = c(L, U)) |>
-    ggplot2:: ggplot(ggplot2::aes(x = n, y = value, color = name)) +
+    dplyr:: mutate(Lower = (mean_resampled_EAF - lower) / mean_resampled_EAF,
+                   Upper = (mean_resampled_EAF - upper) / mean_resampled_EAF) |>
+    tidyr::pivot_longer(cols = c(Lower, Upper)) |>
+    ggplot2::ggplot(ggplot2::aes(x = n, y = value, color = name)) +
     ggplot2::geom_point(alpha = 0.3, pch = 21) +
     ggplot2::geom_smooth(formula = "y ~ x", method = "loess") +
-    ggplot2::scale_fill_manual(values = c("L" = "red", "U" = "#037bcf")) +
-    ggplot2::scale_color_manual(values = c("L" = "red", "U" = "#037bcf"))
+    ggplot2::scale_fill_manual(values = c("Lower" = "red", "Upper" = "#037bcf")) +
+    ggplot2::scale_color_manual(values = c("Lower" = "red", "Upper" = "#037bcf")) +
+    ggplot2::scale_y_log10() +
+    ggplot2::scale_x_log10()
 }

R/plot_source_wads.R

@@ -27,11 +27,7 @@ plot_source_wads <- function(qsip_data,
   WAD <- isotope <- NULL
 
   if (is.null(colors)) {
-    colors <- c(
-      "12C" = "cornflowerblue", "13C" = "firebrick",
-      "14N" = "cornflowerblue", "15N" = "firebrick",
-      "16O" = "cornflowerblue", "18O" = "firebrick"
-    )
+    colors <- isotope_palette
   }
 
   p = qsip_data@source_wads |>

_pkgdown.yml

@@ -60,7 +60,6 @@ reference:
   - plot_feature_resamplings
   - plot_EAF_values
   - plot_growth_values
-  - plot_resampling_convergence
 
 - title: Datasets
   contents:
@@ -110,6 +109,7 @@ reference:
   - calculate_N_light_it
   - calculate_di
   - calculate_bi
+  - plot_resampling_convergence
 
 articles:
 - title: Learn qSIP
@@ -118,6 +118,7 @@ articles:
   - qSIP_workflow
   - filtering
   - resampling
+  - EAF
   - growth
 
 - title: Working with...

data-raw/example_qsip_data.R

@@ -111,7 +111,12 @@ example_qsip_growth_t0 <- get_N_total_it(example_qsip_growth_object, t = 0)
 example_group_dataframe = readxl::read_excel("/Users/kimbrel1/Library/CloudStorage/Dropbox/working/qSIP/multiple_objects_test.xlsx")
 
 
-
+# palettes
+isotope_palette = c(
+  "12C" = "#037bcf", "13C" = "#ff0000",
+  "14N" = "#037bcf", "15N" = "#ff0000",
+  "16O" = "#037bcf", "18O" = "#ff0000"
+)
 
 # save
 usethis::use_data(example_source_df, overwrite = TRUE)
@@ -128,3 +133,5 @@ usethis::use_data(example_qsip_growth_object, overwrite = TRUE)
 usethis::use_data(example_qsip_growth_t0, overwrite = TRUE)
 
 usethis::use_data(example_group_dataframe, overwrite = TRUE)
+
+usethis::use_data(isotope_palette, overwrite = TRUE, internal = TRUE)