germinationmetrics: plot.FourPHFfit – R documentation

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plot.FourPHFfit

Plot the four-parameter hill function fitted cumulative germination curve from a FourPHFfit object

Description

plot.FourPHFfit plots the four-parameter hill function fitted cumulative germination curve (FPHF curve) from a FourPHFfit object as an object of class ggplot. Further, the rate of germination curve (RoG curve) is plotted and different parameters annotated as specified in the different arguments.

Usage

## S3 method for class 'FourPHFfit'
plot(
  x,
  rog = TRUE,
  t50.total = TRUE,
  t50.germ = TRUE,
  tmgr = TRUE,
  mgt = TRUE,
  uniformity = TRUE,
  limits = TRUE,
  plotlabels = TRUE,
  ...
)

Arguments

`x`	An object of class `FourPHFfit` obtained as output from the `FourPHFfit` function.
`rog`	If `TRUE`, plots the Rate of Germination curve (RoG). Default is `TRUE`.
`t50.total`	If `TRUE`, highlights the time required for 50% of total seeds to germinate (\(\textrm{t}_{\textrm{50}_\textrm{Total}}\)) as a vertical line. Default is `TRUE`.
`t50.germ`	If `TRUE`, highlights the time required for 50% of viable/germinated seeds to germinate (\(\textrm{t}_{\textrm{50}_\textrm{Germ}}\)) as a vertical line. Default is `TRUE`.
`tmgr`	If `TRUE`, highlights the Time at Maximum Germination Rate (TMGR) as a vertical line. Default is `TRUE`.
`mgt`	If `TRUE`, highlights the Mean Germination Time (MGT) as a vertical line. Default is `TRUE`.
`uniformity`	If `TRUE`, highlights the uniformity value (\(\textrm{U}_{\textrm{t}_{\textrm{max}}-\textrm{t}_{\textrm{min}}}\)) as a horizontal line. Default is `TRUE`.
`limits`	logical. If `TRUE`, set the limits of y axis (germination percentage) between 0 and 100 in the germination curve plot. If `FALSE`, limits are set according to the data. Default is `TRUE`.
`plotlabels`	logical. If `TRUE`, adds labels to the germination curve plot. Default is `TRUE`.
`...`	Default plot arguments.

Value

The plot of the cumulative germination curve as an object of class ggplot.

Examples

x <- c(0, 0, 0, 0, 4, 17, 10, 7, 1, 0, 1, 0, 0, 0)
y <- c(0, 0, 0, 0, 4, 21, 31, 38, 39, 39, 40, 40, 40, 40)
int <- 1:length(x)
total.seeds = 50

# From partial germination counts
#----------------------------------------------------------------------------
fit1 <- FourPHFfit(germ.counts = x, intervals = int,
                   total.seeds = 50, tmax = 20)

# From cumulative germination counts
#----------------------------------------------------------------------------
fit2 <- FourPHFfit(germ.counts = y, intervals = int,
                   total.seeds = 50, tmax = 20, partial = FALSE)

# Default plots
plot(fit1)
plot(fit2)

# No labels
plot(fit1, plotlabels = FALSE)
plot(fit2, plotlabels = FALSE)

# Only the FPHF curve
plot(fit1, rog = FALSE, t50.total = FALSE, t50.germ = FALSE,
     tmgr = FALSE, mgt = FALSE, uniformity = FALSE)
plot(fit2, rog = FALSE, t50.total = FALSE, t50.germ = FALSE,
     tmgr = FALSE, mgt = FALSE, uniformity = FALSE)

# Without y axis limits adjustment
plot(fit1, limits = FALSE)
plot(fit2, limits = FALSE)

germinationmetrics

Seed Germination Indices and Curve Fitting

v0.1.5

GPL-2 | GPL-3

Authors

J. Aravind [aut, cre] (<https://orcid.org/0000-0002-4791-442X>), S. Vimala Devi [aut], J. Radhamani [aut], Sherry Rachel Jacob [aut], Kalyani Srinivasan [aut], ICAR-NBGPR [cph] (www.nbpgr.ernet.in)

Initial release