Summarise the FvFm and PSII values for each plant line. — summarise

Instead of looking at the distribution of the FvFm or PSII over multiple light pulses across time, we can calculate a mean. Here we plot the mean for these variables as a bar plot with error bars representing SD. As before, the colour is determined by the BASTA selection result.

Usage

summarise_chlorofluoro(data, output_location, width = 25, height = 25)

Arguments

data: data.frame or list of data.frame; data output from computeFvFm_PSIIcomputeFvFm_PSII()
output_location: path; location to save output files
width: numeric; pdf width size. deafult is 18
height: numeric;pdf height size. deafult is 25

Value

Output is also saved as an excel document (one sheet per plate and variable). See output as files "chlorofluoro_plot_3.pdf" and "chlorofluoro_dataset_3.xlsx"

Examples

data("step_one")
data("selection_results")
output_location <- tempdir()
output_location <- "/Users/kejc/"
step_three <- summarise_chlorofluoro(step_one, output_location)
#> Joining with `by = join_by(Plant_ID)`
#> Joining with `by = join_by(Plant_ID)`
#> Joining with `by = join_by(Plant_ID)`
#> Joining with `by = join_by(Plant_ID)`
#> Joining with `by = join_by(Plant_ID)`
#> Joining with `by = join_by(Plant_ID)`
#> Joining with `by = join_by(Plant_ID)`
#> Joining with `by = join_by(Plant_ID)`
#> Warning: cannot create file '/Users/kejc//chlorofluoro_dataset_3.xlsx', reason 'No such file or directory'
#> Data saved to /Users/kejc//chlorofluoro_dataset_3.xlsx
#> Error in pdf(file.path(output_location, "chlorofluoro_plot_3.pdf"), width = width,     height = height): cannot open file '/Users/kejc//chlorofluoro_plot_3.pdf'