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plotting fluxes for visual evaluation

Source: R/flux_plot.R
flux_plot.Rd

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,
  conc_col,
  datetime_col,
  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 = "",
  facet_wrap_args = list(ncol = 4, nrow = 3, scales = "free"),
  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

conc_col

column with gas concentration

datetime_col

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

facet_wrap_args

list of arguments for facet_wrap_paginate

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)

ggsave_args

list of arguments for ggsave (in case output = "ggsave")

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(slopes0_flag)
flux_plot(slopes0_flag, conc, datetime)
#> Plotting in progress

data(slopes30lin_flag)
flux_plot(slopes30lin_flag, conc, datetime)
#> Plotting in progress

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