plot.FourPHFfit.bulk {germinationmetrics}

Plot the multiple four-parameter hill function fitted cumulative germination curves from a FourPHFfit.bulk object

Description

plot.FourPHFfit plots multiple four-parameter hill function fitted cumulative germination curves (FPHF curves) or the rate of germination curves (RoG curves) from a FourPHFfit.bulk object as an object of class ggplot. Further, either one of the parameters such as time required for 50% of total seeds to germinate (\(\textrm{t}_{\textrm{50}_\textrm{Total}}\)), time required for 50% of viable/germinated seeds to germinate (\(\textrm{t}_{\textrm{50}_\textrm{Germ}}\)), Time at Maximum Germination Rate (TMGR), Mean Germination Time (MGT), or uniformity value (\(\textrm{U}_{\textrm{t}_{\textrm{max}}-\textrm{t}_{\textrm{min}}}\)) can also be annotated in the plot as specified in the annotate argument.

Usage

## S3 method for class 'FourPHFfit.bulk'
plot(
  x,
  rog = FALSE,
  annotate = c("none", "t50.total", "t50.germ", "tmgr", "mgt", "uniformity"),
  limits = TRUE,
  group.col,
  show.points = FALSE,
  ...
)

Arguments

x

An data frame object of class FourPHFfit.bulk obtained as output from the FourPHFfit.bulk function.

rog

If TRUE, plots the Rate of Germination curves (RoG) instead of the Four-Parameter Hill Function fitted cumulative germination curves (FPHF). Default is FALSE.

annotate

The parameter to be annotated in the plot. Either "t50.total" (\(\textrm{t}_{\textrm{50}_\textrm{Total}}\)), "t50.germ" (\(\textrm{t}_{\textrm{50}_\textrm{Germ}}\)), "tmgr" (TMGR), "mgt" (MGT), or "uniformity" (\(\textrm{U}_{\textrm{t}_{\textrm{max}}-\textrm{t}_{\textrm{min}}}\)). All the parameters are annotated as vertical lines, except for (\(\textrm{U}_{\textrm{t}_{\textrm{max}}-\textrm{t}_{\textrm{min}}}\)), which is annotated as horizontal lines.

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.

group.col

The names of the column in data frame x according to which grouping has to be done.

show.points

logical. If TRUE, shows the original data points (only for the FPHF curve). Default is TRUE.

...

Default plot arguments.

Value

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

See Also

FourPHFfit.bulk

Examples

data(gcdata)

counts.per.intervals <- c("Day01", "Day02", "Day03", "Day04", "Day05",
                          "Day06", "Day07", "Day08", "Day09", "Day10",
                          "Day11", "Day12", "Day13", "Day14")

fits <- FourPHFfit.bulk(gcdata, total.seeds.col = "Total Seeds",
                    counts.intervals.cols = counts.per.intervals,
                    intervals = 1:14, partial = TRUE,
                    fix.y0 = TRUE, fix.a = TRUE, xp = c(10, 60),
                    tmax = 20, tries = 3, umax = 90, umin = 10)

# Plot FPHF curves
plot(fits, group.col = "Genotype")

# Plot ROG curves
plot(fits, rog = TRUE, group.col = "Genotype")

# Plot FPHF curves with points
plot(fits, group.col = "Genotype", show.points = TRUE)

# Plot FPHF curves with annotations
plot(fits, group.col = "Genotype", annotate = "t50.total")
plot(fits, group.col = "Genotype", annotate = "t50.germ")
plot(fits, group.col = "Genotype", annotate = "tmgr")
plot(fits, group.col = "Genotype", annotate = "mgt")
plot(fits, group.col = "Genotype", annotate = "uniformity")

# Plot ROG curves with annotations
plot(fits, rog = TRUE, group.col = "Genotype", annotate = "t50.total")
plot(fits, rog = TRUE, group.col = "Genotype", annotate = "t50.germ")
plot(fits, rog = TRUE, group.col = "Genotype", annotate = "tmgr")
plot(fits, rog = TRUE, group.col = "Genotype", annotate = "mgt")
plot(fits, rog = TRUE, group.col = "Genotype", annotate = "uniformity")



# Change colour of curves using ggplot2 options
library(ggplot2)
curvesplot <- plot(fits, group.col = "Genotype")

# 'Dark2' palette from RColorBrewer
curvesplot + scale_colour_brewer(palette = "Dark2")

# Manual colours
curvesplot +
  scale_colour_manual(values = c("Coral", "Brown", "Blue",
                                 "Aquamarine", "Red"))