flux_plot: Plotting fluxes for visual evaluation

In fluxible: Ecosystem Gas Fluxes Calculations for Closed Loop Chamber Setup

Plotting fluxes for visual evaluation

Description

Plots the fluxes, fit and slope in facets with color code indicating quality flags This function takes time to run and is optional in the workflow, but it is still highly recommended to use it to visually check the measurements. Note that 'flux_plot' is specific to the fluxible package and will work best with datasets produced following a fluxible workflow.

Usage

flux_plot(
  slopes_df,
  f_conc = f_conc,
  f_datetime = f_datetime,
  color_discard = "#D55E00",
  color_cut = "#D55E00",
  color_ok = "#009E73",
  color_zero = "#CC79A7",
  scale_x_datetime_args = list(date_breaks = "1 min", minor_breaks = "10 sec",
    date_labels = "%e/%m \n %H:%M"),
  f_ylim_upper = 800,
  f_ylim_lower = 400,
  f_plotname = "",
  f_facetid = "f_fluxid",
  facet_wrap_args = list(ncol = 4, nrow = 3, scales = "free"),
  longpdf_args = list(ncol = 4, width = 29.7, ratio = 1),
  y_text_position = 500,
  print_plot = "FALSE",
  output = "print_only",
  ggsave_args = list()
)

Arguments

slopes_df	dataset containing slopes, with flags produced by flux_quality
f_conc	column with gas concentration
f_datetime	column with datetime of each data point
color_discard	color for fits with a discard quality flag
color_cut	color for the part of the flux that is cut
color_ok	color for fits with an ok quality flag
color_zero	color for fits with a zero quality flag
scale_x_datetime_args	list of arguments for scale_x_datetime
f_ylim_upper	y axis upper limit
f_ylim_lower	y axis lower limit
f_plotname	filename for the extracted pdf file; if empty, the name of slopes_df will be used
f_facetid	character vector of columns to use as facet IDs. Note that they will be united, and that has to result in a unique facet ID for each measurement. Default is f_fluxid
facet_wrap_args	list of arguments for facet_wrap, also used by facet_wrap_paginate in case ⁠output = "pdfpages⁠
longpdf_args	arguments for longpdf in the form ⁠list(ncol, width (in cm), ratio)⁠
y_text_position	position of the text box
print_plot	logical, if TRUE it prints the plot as a ggplot object but will take time depending on the size of the dataset
output	"pdfpages", the plots are saved as A4 landscape pdf pages; "ggsave", the plots can be saved with the ggsave function; "print_only" (default) prints the plot without creating a file (independently from print_plot being TRUE or FALSE); "longpdf", the plots are saved as a pdf file as long as needed (faster than "pdfpages")
ggsave_args	list of arguments for ggsave (in case output = "ggsave")

Details

output = "pdfpages" uses facet_wrap_paginate, which tends to be slow and heavy. With ⁠output = "longpdf⁠, a long single page pdf is exported. Default width is 29.7 cm (A4 landscape) and is will be as long as it needs to be to fit all the facets. The arguments ncol and ratio in longpdf_args specify the number of columns and the ratio of the facet respectively. This method is considerably faster than pdfpages, because it bypasses facet_wrap_paginate, but is a bit less aesthetic.

Value

plots of fluxes, with raw concentration data points, fit, slope, and color code indicating quality flags and cuts. The plots are organized in facets according to flux ID, and a text box display the quality flag and diagnostics of each measurement. The plots are returned as a ggplot object if print_plot = TRUE; if print_plot = FALSE it will not return anything but will produce a file according to the output argument.

Examples

data(co2_conc)
slopes <- flux_fitting(co2_conc, conc, datetime, fit_type = "exp_zhao18")
slopes_flag <- flux_quality(slopes, conc)
flux_plot(slopes_flag, conc, datetime)

fluxible documentation built on Sept. 12, 2025, 1:08 a.m.