germinationmetrics: plot.FourPHFfit.bulk – R documentation

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plot.FourPHFfit.bulk

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.

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"))

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