get_pdf_with_cell_length_fit_plots: Make a pdf containing the cell length fits.
In impres-lab/leafkin: Leaf kinematic analysis in R

View source: R/get_pdf_with_cell_length_fit_plots.R

get_pdf_with_cell_length_fit_plots

R Documentation

Make a pdf containing the cell length fits.

Description

Produces a pdf file in the work directory, containing all the graphs of the fitted cell lengths and their derivatives.

Usage

get_pdf_with_cell_length_fit_plots(
  cell_length_data,
  interval_in_cm = 0.1,
  bw_multiplier = 1,
  output_bw_tibble = FALSE
)

Arguments

`cell_length_data`	data.frame or tibble containing the cell length data.
`interval_in_cm`	specifies the inteval in centimetre at which cell lengths should be calculated (default = 0.1).
`bw_multiplier`	multiplies the calculated bandwidth with the provided number (default = 1).
`output_bw_tibble`	`FALSE` by default. When `TRUE`, the function will return all calculated bandwidths as a tibble.

Details

This function takes in cell length data. The provided cell length data must be in a data.frame or tibble. The first column contains the plant IDs (header = plant_id). The second column contains the positions of the cell length measurements in the leaf's growth zone (in cm) (header = position). The third column contains the cell length measurements (header = cell_length).

Important: Cell length measurements of each plant are thus directly underneath eachother in the provided data.

Concerning the variables: Using the interval_in_cm variable, you indicate how often (i.e. at which interval) a cell length should be calculated over the entire growth zone. By default, it is set to 0.1 cm.

The bw_multiplier can be used to multiply the bandwidth. Usually, the calculated bandwidth is OK to use. Multiplying it by a number between 0 and 1 will follow the profile more strict. Multiplying the bandwidth with a number larger than 1 will make the fit more loose. Making the multiplier to small or to big could result in an error.

The function will always produce a pdf file with plots in the working directory, also indicating the multiplier in the file name. If you set output_bw_tibble to TRUE, then the function will also return all calculated bandwidths as a tibble.