licorplots: Plot Li-COR data

In lbmountain/licornetics: Plot and calculate physiological parameters using LI-COR data

Plot Li-COR data

Description

Creates plots for physiological parameters measured using the Li-COR photosystem.

Usage

licorplots(
  identifier,
  type = "gsw",
  area_correction = 1,
  stomden = NULL,
  timestamps = NULL,
  timeframe = NULL,
  y_axis_limits = NULL,
  errorbars = "se",
  legend_title = "Genotype",
  legend_labels = identifier,
  remove_outliers = "no",
  colours = NULL,
  axis_label = type
)

Arguments

identifier	Keywords that distinguish the Li-COR .xlsx files for the different datasets (e.g. "wt", "mutant1").
type	Determines y axis data. Can be "gsw" (absolute stomatal conductance), "relgsw" (relative stomatal conductance), "A" (CO2 assimilation), "WUE" (intrinsic water use efficiency), "Ci" (Intercellular CO2) or "Ca" (Ambient CO2). From version 2.0.1 onward also allows plotting of other columns (e.g. "Fs").
area_correction	Li-COR chamber size divided by average of total measured leaf areas (only one value). Default is set to 1.
stomden	Insert stomatal density to normalise values by stomatal density.
timestamps	Optionally add vertical lines to the plot as timeline indicators (e.g. 'c(20, 40, 60)').
timeframe	Crop the range of time you want to show (e.g. '16:70').
y_axis_limits	Change the y axis limits (e.g. 'c(0,2)' with 0 being the lower and 2 the upper limit).
errorbars	Set type of errorbars to either standard error ("se", this is the default) or standard deviation ("sd").
legend_title	Change the title of the legend. Default is set to "Genotype".
legend_labels	Change the labels within the legend. Default is set to the input given by the 'identifier' argument.
remove_outliers	Optionally remove boxplot outliers by setting to "yes" (based on outliers from the 'A' column).
colours	Set colour palette (e.g. 'c("red", "green")'). Default uses the "Isfahan1" palette of the MetBrewer package.
axis_label	Change y axis label text. Allows markdown language elements.

lbmountain/licornetics documentation built on April 11, 2024, 3:51 p.m.