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

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.

See also

FourPHFfit

Examples

# \donttest{
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)
#> Warning: All aesthetics have length 1, but the data has 14 rows.
#> ℹ Please consider using `annotate()` or provide this layer with data containing
#>   a single row.
#> Warning: All aesthetics have length 1, but the data has 14 rows.
#> ℹ Please consider using `annotate()` or provide this layer with data containing
#>   a single row.

plot(fit2)
#> Warning: All aesthetics have length 1, but the data has 14 rows.
#> ℹ Please consider using `annotate()` or provide this layer with data containing
#>   a single row.
#> Warning: All aesthetics have length 1, but the data has 14 rows.
#> ℹ Please consider using `annotate()` or provide this layer with data containing
#>   a single row.


# No labels
plot(fit1, plotlabels = FALSE)
#> Warning: All aesthetics have length 1, but the data has 14 rows.
#> ℹ Please consider using `annotate()` or provide this layer with data containing
#>   a single row.
#> Warning: All aesthetics have length 1, but the data has 14 rows.
#> ℹ Please consider using `annotate()` or provide this layer with data containing
#>   a single row.

plot(fit2, plotlabels = FALSE)
#> Warning: All aesthetics have length 1, but the data has 14 rows.
#> ℹ Please consider using `annotate()` or provide this layer with data containing
#>   a single row.
#> Warning: All aesthetics have length 1, but the data has 14 rows.
#> ℹ Please consider using `annotate()` or provide this layer with data containing
#>   a single row.


# 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)
#> Warning: All aesthetics have length 1, but the data has 14 rows.
#> ℹ Please consider using `annotate()` or provide this layer with data containing
#>   a single row.
#> Warning: All aesthetics have length 1, but the data has 14 rows.
#> ℹ Please consider using `annotate()` or provide this layer with data containing
#>   a single row.

plot(fit2, limits = FALSE)
#> Warning: All aesthetics have length 1, but the data has 14 rows.
#> ℹ Please consider using `annotate()` or provide this layer with data containing
#>   a single row.
#> Warning: All aesthetics have length 1, but the data has 14 rows.
#> ℹ Please consider using `annotate()` or provide this layer with data containing
#>   a single row.

# }