Merge pull request #61 from Plant-Functional-Trait-Course/next_version

Next version

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: fluxible
 Title: Ecosystem Gas Fluxes Calculations for Closed Loop Chamber Setup
-Version: 0.0.2
-Date: 2024-08-28
+Version: 0.0.3
+Date: 2024-09-03
 Authors@R: 
     c(person(given = "Joseph", family = "Gaudard", , "joseph.gaudard@pm.me", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0002-6989-7624")),

NAMESPACE

@@ -38,8 +38,11 @@ importFrom(ggplot2,geom_point)
 importFrom(ggplot2,geom_text)
 importFrom(ggplot2,ggplot)
 importFrom(ggplot2,ggsave)
+importFrom(ggplot2,guide_legend)
+importFrom(ggplot2,guides)
 importFrom(ggplot2,labs)
 importFrom(ggplot2,scale_color_manual)
+importFrom(ggplot2,scale_linetype_manual)
 importFrom(ggplot2,scale_x_datetime)
 importFrom(ggplot2,theme_bw)
 importFrom(ggplot2,ylim)
@@ -58,6 +61,7 @@ importFrom(stringr,str_c)
 importFrom(tidyr,drop_na)
 importFrom(tidyr,fill)
 importFrom(tidyr,nest)
+importFrom(tidyr,pivot_longer)
 importFrom(tidyr,pivot_wider)
 importFrom(tidyr,replace_na)
 importFrom(tidyr,unnest)

NEWS.md

@@ -1,5 +1,5 @@
-# fluxible 0.0.2
+# fluxible 0.0.3
 
-* Unit choices in flux_calc
-* plot_area can be a variable in flux_calc
-* flux_fitting with exponential model works when concentration data are missing in the middle of the measurement
+* All plots are colored the same (colors code for raw condentration data points and fit and slope in black)
+* Legend for line types in plots
+* Plot subtitles indicating the fit type

R/flux_plot.R

@@ -35,15 +35,17 @@
 #' @importFrom dplyr rename select distinct mutate
 #' @importFrom ggplot2 ggplot aes geom_point geom_line scale_color_manual
 #' scale_x_datetime ylim facet_wrap labs geom_text theme_bw ggsave
+#' scale_linetype_manual guides guide_legend
 #' @importFrom ggforce facet_wrap_paginate n_pages
 #' @importFrom purrr quietly
 #' @importFrom progress progress_bar
 #' @examples
 #' data(slopes0_flag)
-#' flux_plot(slopes0_flag, output = "print_only")
+#' flux_plot(slopes0_flag)
 #' data(slopes30lin_flag)
-#' flux_plot(slopes30lin_flag, output = "print_only")
-#' flux_plot(slopes30qua_flag, output = "print_only")
+#' flux_plot(slopes30lin_flag)
+#' data(slopes30qua_flag)
+#' flux_plot(slopes30qua_flag)
 #' @export
 
 flux_plot <- function(slopes_df,
@@ -169,6 +171,12 @@ flux_plot <- function(slopes_df,
   message("Plotting in progress")
 
   f_plot <- f_plot +
+    geom_line(
+      aes(y = .data$fit, linetype = .data$linetype),
+      linewidth = 0.3,
+      na.rm = TRUE,
+      show.legend = TRUE
+    ) +
     scale_color_manual(values = c(
       "cut" = ((color_cut)),
       "ok" = ((color_ok)),
@@ -178,6 +186,10 @@ flux_plot <- function(slopes_df,
       "weird_flux" = ((color_discard)),
       "force_ok" = ((color_ok))
     )) +
+    scale_linetype_manual(values = c(
+      "fit" = "longdash",
+      "slope" = "dashed"
+    )) +
     scale_x_datetime(
       date_breaks = ((f_date_breaks)), minor_breaks = ((f_minor_breaks)),
       date_labels = ((f_date_labels))
@@ -188,10 +200,13 @@ flux_plot <- function(slopes_df,
     ) +
     labs(
       title = "Fluxes quality assessment",
+      subtitle = paste(fit_type, "model"),
       x = "Datetime",
       y = "Concentration",
-      colour = "Quality flags"
-    )
+      colour = "Quality flags",
+      linetype = "Fits"
+    ) +
+    guides(color = guide_legend(override.aes = list(linetype = 0)))
 
   if (((output)) == "print_only") {
     return(f_plot)

R/flux_plot_exp.R

@@ -10,6 +10,7 @@
 #' @importFrom ggforce facet_wrap_paginate n_pages
 #' @importFrom purrr quietly
 #' @importFrom grDevices pdf dev.off
+#' @importFrom tidyr pivot_longer
 
 
 
@@ -26,7 +27,16 @@ flux_plot_exp <- function(slopes_df,
     cut_arg = ((cut_arg))
   )
 
-
+  slopes_df <- slopes_df |>
+    rename(
+      fit = "f_fit",
+      slope = "f_fit_slope"
+    ) |>
+    pivot_longer(
+      cols = c("fit", "slope"),
+      names_to = "linetype",
+      values_to = "fit"
+    )
 
 
 
@@ -38,18 +48,6 @@ flux_plot_exp <- function(slopes_df,
       size = 0.2,
       na.rm = TRUE
     ) +
-    geom_line(
-      aes(y = .data$f_fit),
-      linetype = "longdash",
-      linewidth = 0.3,
-      na.rm = TRUE
-    ) +
-    geom_line(
-      aes(y = .data$f_fit_slope),
-      linetype = "dashed",
-      linewidth = 0.2,
-      na.rm = TRUE
-    ) +
     geom_text(
       aes(x = .data$f_start, y = ((y_text_position)), label = .data$print_col),
       vjust = 0, hjust = "inward",

R/flux_plot_lin.R

@@ -23,6 +23,11 @@ flux_plot_lin <- function(slopes_df,
     cut_arg = ((cut_arg))
   )
 
+  slopes_df <- slopes_df |>
+    mutate(
+      fit = .data$f_fit,
+      linetype = "fit"
+    )
 
   plot_lin <- slopes_df |>
     ggplot(aes(.data$f_datetime)) +
@@ -31,11 +36,6 @@ flux_plot_lin <- function(slopes_df,
       size = 0.2,
       na.rm = TRUE
     ) +
-    geom_line(
-      aes(y = .data$f_fit),
-      linetype = "longdash",
-      na.rm = TRUE
-    ) +
     geom_text(
       aes(
         x = .data$f_start, y = ((y_text_position)),

R/flux_plot_quadratic.R

@@ -10,22 +10,44 @@
 #' @importFrom ggforce facet_wrap_paginate n_pages
 #' @importFrom purrr quietly
 #' @importFrom grDevices pdf dev.off
+#' @importFrom tidyr pivot_longer
 
 
 
 flux_plot_quadratic <- function(slopes_df,
                                 y_text_position = 500,
                                 cut_arg = "cut") {
-  plot_quadratic <- slopes_df |>
-    flux_plot_lin(
-      y_text_position = ((y_text_position)),
-      cut_arg = ((cut_arg))
+  param_df <- flux_param_lm(((slopes_df)), cut_arg = ((cut_arg)))
+
+  slopes_df <- flux_plot_flag(((slopes_df)),
+    ((param_df)),
+    cut_arg = ((cut_arg))
+  )
+
+  slopes_df <- slopes_df |>
+    rename(
+      fit = "f_fit",
+      slope = "f_fit_slope"
+    ) |>
+    pivot_longer(
+      cols = c("fit", "slope"),
+      names_to = "linetype",
+      values_to = "fit"
     )
 
-  plot_quadratic <- plot_quadratic +
-    geom_line(
-      aes(y = .data$f_fit_slope, color = .data$f_quality_flag),
-      linetype = "dashed",
+  plot_quadratic <- slopes_df |>
+    ggplot(aes(.data$f_datetime)) +
+    theme_bw() +
+    geom_point(aes(y = .data$f_conc, color = .data$f_quality_flag),
+      size = 0.2,
+      na.rm = TRUE
+    ) +
+    geom_text(
+      aes(
+        x = .data$f_start, y = ((y_text_position)),
+        label = .data$print_col
+      ),
+      vjust = 0, hjust = "inward",
       na.rm = TRUE
     )