read_mecmesin_tab_list: read_mecmesin_tab_list

In tbgitoo/textureAnalyzerGels: Reading and analyzing texture analyzer data

read_mecmesin_tab_list

Description

Reads a series of texture analyzer tab files

Usage

read_mecmesin_tab_list(file_info,root_folder=getwd(),folder_column="Folder",file_column="File",
sample_diameter_column="diameter_mm",do_plot=TRUE,do_smoothing=TRUE,lines_to_read=NULL,downup=TRUE,...)

Arguments

file_info	Dataframe describing the files to be read. Needs to contain at least the following columns: 1. A folder column, describing the sub-folder where the individual files are located. The name of this column is given by the argument folder_column. 2. A file column indicating the filename of the file to be read. The name of this column is given by file_column. 3. A sample or gel diameter column, where the diameter of the sample or gel is indicated (whichever is smaller, basically). The name of this column is given by the sample_diameter_column argument.
root_folder	Common root folder where all the tab-files to be read are located, defaults to the current working directory as given by getwd.
folder_column	Name of the column in file_info that contains the folder location.
file_column	Name of the column in file_info that contains the filename.
sample_diameter_column	Name of the column in file_info that contains the relevant sample/gel diameters. The sample or gel diameters should be in millimeters.
do_plot	Indicates whether or not plots should be drawn while reading the files
do_smoothing	Indicates whether or not smoothing by smooth_texture_analyzer_data should be performed when reading the files
lines_to_read	Possibility to restrict the lines to be read, a numerical vector indicating the lines to be read.
downup	sample displacement down (compression) followed by equal movement up (release)?
...	Additional arguments to be passed to smooth_texture_analyzer_data. These arguments should be named according to the arguments given in smooth_texture_analyzer_data

Details

The function will run through all the lines of file_info and read the file specified by the file and folder columns (which need to be located within folder given by the root_folder argument). To do so, it uses read_mecmesin_tab, and, if do_smoothing is TRUE, smooth_texture_analyzer_data as well. If do_plot is true, it will plot the data for each line as well. The lines_to_read argument can be used to restrict the file reading to certain lines; this is primarily for debugging purposes, as the function may take quite a long time if there are many entries in file_info.

Value

A list with as many elements as there are rows in file_info. Each element in the list is the output of read_mecmesin_tab, optionally processed by smooth_texture_analyzer_data

Author(s)

Thomas Braschler, Patrick Burch

References

Filippova A, Bonini F, Efremov L, Locatelli M, Preynat-Seauve O, Beduer A, Krause KH, Braschler T, 2021: Neurothreads: development of supportive carriers for mature dopaminergic neuron differentiation and implantation, Raw data set: https://doi.org/10.5281/zenodo.4441090 accompanying the corresponding scientific publication at Biomaterials (https://doi.org/10.1016/j.biomaterials.2021)

Examples

# The data for this example is taken from https://doi.org/10.5281/zenodo.4441090 (Filippova et al. 2021), Supplementary_Fig_S6.zip, sample2 and sample3 for the traction test. From there, we copied the file "raw-TensileStrenght(peellike)(V1)-Modified Version-sample-2.txt" and "raw-TensileStrenght(peellike)(V1)-Modified Version-sample-3.txt" data files, as well as the file listing "files_stretch.xlsx" for these two data files here to serve as an example.
path = system.file('sampleData/mecmesin', package = 'textureAnalyzerGels');
tensile_test_file_info = read.xls(file.path(path,"files_stretch.xlsx") )
tensile_test_data=read_mecmesin_tab_list(tensile_test_file_info,root_folder=path,do_smoothing=TRUE,do_plot=TRUE,downup=FALSE,sd=0.1)

tbgitoo/textureAnalyzerGels documentation built on March 30, 2022, 4:53 a.m.