Germination count data
An example germination count dataset. It includes germination count data over 14 days from five genotypes (G1 to G5) in three replications
gcdata
A data frame with 17 columns:
The genotype.
Replication.
Number of seeds that germinated (germination counts) on Day 1.
Number of seeds that germinated (germination counts) on Day 2.
Number of seeds that germinated (germination counts) on Day 3.
Number of seeds that germinated (germination counts) on Day 4.
Number of seeds that germinated (germination counts) on Day 5.
Number of seeds that germinated (germination counts) on Day 6.
Number of seeds that germinated (germination counts) on Day 7.
Number of seeds that germinated (germination counts) on Day 8.
Number of seeds that germinated (germination counts) on Day 9.
Number of seeds that germinated (germination counts) on Day 10.
Number of seeds that germinated (germination counts) on Day 11.
Number of seeds that germinated (germination counts) on Day 12.
Number of seeds that germinated (germination counts) on Day 13.
Number of seeds that germinated (germination counts) on Day 14.
Total number of seeds tested.
data(gcdata)
library(ggplot2)
library(reshape2)
# Plot partial germination counts over time
#----------------------------------------------------------------------------
# Convert wide-from to long-form
gcdatamelt <- melt(gcdata[, !names(gcdata) %in% c("Total Seeds")],
id.vars = c("Genotype", "Rep"))
ggplot(gcdatamelt, aes(x = variable, y = value,
group = interaction(Genotype, Rep),
colour = Genotype)) +
geom_point(alpha = 0.7) +
geom_line(alpha = 0.7) +
ylab("Germination count (Partial)") +
xlab("Intervals") +
theme_bw()
# Plot partial germination counts over time
#----------------------------------------------------------------------------
# Convert wide-from to long-form
# Compute cumulative germination counts
gcdata2 <- gcdata
gcdata2[, !names(gcdata2) %in% c("Genotype", "Rep", "Total Seeds")] <-
t(apply(gcdata2[, !names(gcdata2) %in% c("Genotype", "Rep", "Total Seeds")], 1, cumsum))
gcdatamelt2 <- melt(gcdata2[, !names(gcdata2) %in% c("Total Seeds")],
id.vars = c("Genotype", "Rep"))
ggplot(gcdatamelt2, aes(x = variable, y = value,
group = interaction(Genotype, Rep),
colour = Genotype)) +
geom_point(alpha = 0.7) +
geom_line(alpha = 0.7) +
ylab("Germination count (Cumulative)") +
xlab("Intervals") +
theme_bw()
# Compute germination indices
#----------------------------------------------------------------------------
counts.per.intervals <- c("Day01", "Day02", "Day03", "Day04", "Day05",
"Day06", "Day07", "Day08", "Day09", "Day10",
"Day11", "Day12", "Day13", "Day14")
germination.indices(gcdata, total.seeds.col = "Total Seeds",
counts.intervals.cols = counts.per.intervals,
intervals = 1:14, partial = TRUE, max.int = 5)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.