plot_gr_microplate: Function to plot growth rates over microplate frame.

In MartinBanchero/mpxtractor: Process microplate reader output files into a tidy dataframe

Function to plot growth rates over microplate frame.

Description

This function takes a dataframe with the raw data and the information from the layout file. Calculate growth rate and plot this growth rates over a microplate frame.

Usage

plot_gr_microplate(
  df_data,
  var_gr,
  exp_title = NULL,
  ws,
  cond_to_col,
  plate_file = NULL,
  output_filename
)

Arguments

df_data	Is a dataframe that combines data files with layout files
var_gr	This the attribute to be used to calculate growth rates
exp_title	optional, add the title.
ws	is the windowsize in hours
cond_to_col	The condition from the layout to color
plate_file	plate file to be use to compute growth rates in case of multiple files.
output_filename	The name of the output file followed by proper extension, ie. .png

Value

Returns the background plot which is the microplate frame and over this the plot of growth rates in each well. The background plot shows in the x-axis the number of columns and in the y-axis the letter to identified the row.

Warning

Note that the time should be a time series, if the time series is broken the growth rates are not calculated and the process stop.

Examples

## Not run: 
# Get the data file path
file_path_sp <- system.file(
 "extdata",
 "test_gr_spectramax.txt",
 package = "mpxtractor"
)

# Extract the data stored in the files into a df using proper wrangling function
df_sp <- mpxtractor::read_spectramax_data(
 file = file_path_sp
 )
 # get the path to layout file
file_path_layout <- system.file(
 "extdata", "test_layout_file.csv",
 package = "mpxtractor"
)
# combine raw data with layout scheme
df_data_combine <- mpxtractor::combine_data_with_layout(
 df_data = df_sp,
 reader_type = "spectramax",
 layout_files = file_path_layout
)

microplateplot <- mpxtractor::plot_gr_microplate(
 df_data = df_data_combine,
 var_gr = "Measurement",
 exp_title = "Spectramax experiment",
 ws = "2hs",
 cond_to_col = "condition",
 output_filename = "growth_rates_test.png")

## End(Not run)
#Check vignette **plotting_functions()** for more information.

MartinBanchero/mpxtractor documentation built on March 30, 2022, 10:56 p.m.