plotting fluxes for visual evaluation — flux

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.

Usage

flux_plot(
  slopes_df,
  color_discard = "#D55E00",
  color_cut = "#D55E00",
  color_ok = "#009E73",
  color_zero = "#CC79A7",
  f_date_breaks = "1 min",
  f_minor_breaks = "10 sec",
  f_date_labels = "%e/%m \n %H:%M",
  f_ylim_upper = 800,
  f_ylim_lower = 400,
  f_plotname = "plot_quality",
  facet_wrap_args = list(ncol = 4, nrow = 3, scales = "free"),
  y_text_position = 500,
  print_plot = "FALSE",
  output = "print_only",
  ggsave_args = list(),
  cut_arg = "cut",
  no_data_flag = "no_data"
)

Arguments

slopes_df: dataset containing slopes, with flags produced by flux_quality
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
f_date_breaks: date_breaks argument for scale_x_datetime
f_minor_breaks: minor breaks argument for scale_x_datetime
f_date_labels: date_labels argument 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
facet_wrap_args: list of arguments for facet_wrap_paginate
y_text_position: position of the text box
print_plot: FALSE or TRUE, if TRUE it prints the plot in R 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)
ggsave_args: list of arguments for ggsave (in case output = "ggsave")
cut_arg: argument pointing rows to be cut from the measurements
no_data_flag: flag marking fluxID without data in f_quality_flag

Value

a ggplot object if print_plot = TRUE, if print_plot = FALSE it will not return anything but will produce a file depending on output

Examples

data(slopes0_flag)
flux_plot(slopes0_flag)
#> Plotting in progress

data(slopes30lin_flag)
flux_plot(slopes30lin_flag)
#> Plotting in progress

data(slopes30qua_flag)
flux_plot(slopes30qua_flag)
#> Part of the fit will not be displayed
#>     because f_ylim_lower is too high.
#> Plotting in progress