7 EcophyCofog Package

A package to handle routinely produced raw outputs of the CIRAS-3, MINIPAM II and PSYPRO of EcoFog’s ecophysiology lab.

Package written by Tristan LAFONT RAPNOUIL and hosted on github. Can be installed running:

install.packages("devtools")
library(devtools)
install_github("https://github.com/LafontRapnouilTristan/EcophyCofog")

7.1 Utilitaries

7.1.1 Library

Used to load install (if required) and load multiple package at once.

usage:

EcophyCofog::Library(c("pckg1", "pckg2", "pckg3"))

7.1.2 NotIn

A custom operator to test the differences between vectors.

x <- c("a", "b", "c")
y <- c("d", "a", "e")
x %notin% y

[1] FALSE TRUE TRUE

7.1.3 xtract_legend

Store the legend of a ggplot object.

legend <- xtract_legend(myggplot)

7.1.4 dummy_data

Create a meaningless numeric data frame for testing things.

data <- dummy_data(nbcol = 4, nbrow = 100)

7.2 MiniPAM

7.2.1 merge_minipam

Merge several miniPAM output files. All files should be stored in one folder, and only them!! See Fluorescence for more details.

library(EcophyCofog)
input_path <- PATH_TO_THE_FOLDER
filename <- NAME_OF_THE_MERGED_OUTPUT
merge_minipam(input_path, filename)

7.2.2 minipam

Take as input a csv dataframe containing output of the minipam. For ETR and Fv/Fm measurements only. And return clean files containing each type of measurements + the ETR curves.

library(EcophyCofog)
Name_of_the_input_file <- NAME_OF_YOUR_MERGED_FILE
input_path <- PATH_TO_SAID_FILE
path_to_ID_match <- PATH_TO_YOUR_ID_MATCH_FILE
minipam(Name_of_the_input_file, input_path, path_to_ID_match)

7.3 CIRAS-3

7.3.1 merge_ciras

Used to merge all ciras output of a foled into one file.

path_to_xls a character string with your path to all your ciras .xls output. Their name must always end as _treatment_sampleID.xls (e.g. CIRAS_3_Aechmea m _DP_1.xls). skip: the number of useless rows at the top of your .xls file, Jean-Yves Goret template have three.

merge_ciras(path_to_xls, skip = 3)

7.4 PSYPRO

7.4.1 psypro

Transform psypro output files into csv dataframe with mean water potential of your triplicate. param usedset the predetermined name of your set 0,1,2 or 3. param lim min and max values expected out of the psypro for you samples. Used to standardized graphs for faster reading. Discuss with lab members to understand!! param ID_vec a vector of length 8 (number of sensors) with your samples’ ID. Empty sensors are named 0!! param path_to_calibration path to you calibration file. param psypro_output path to your psypro output.

psypro(usedset, lim = c(-3, 2), ID_vec, path_to_calibration,
    psypro_output)

7.5 PASCO

7.5.1 PASCO_transfo

An earlier version of PASCO_transfo2, should not be used anymore.

7.5.2 PASCO_transfo2

Process the PASCO probe output csv to get the gasfluxes.

param data a data frame output from Sparkview (usually read from .csv) param ech a character vector with either the probe or sample name param name_run a character vector with the name of all your runs (e.g., c(“stab1”,“RECO”,“NEE”)) param select a numeric vector of the runs you want to keep (e.g., c(2,3)) param A the Area param V the Volume

PASCO_transfo2(data, ech, name_run, select, A = 1, V = 5)

7.6 PCR layout

Functions to create excel files containing the PCR plate layout (with controls and all) from your sample list. Both for sample names and then tags combination.

7.6.1 plate_layout

param samples a vector containing all your samples ID, they will fill the plate in the order they are in this vector, when having replicates for one sample, plz index them as “SampleName 1” to “SampleName N” and not “SampleName_X” or “SampleName.X”. param proj name of your project to name your plates as : “proj-PLx” param name_file a name to your output file param save_file_path path to where you want to save the excel output param starting_plate_number where from start plate numbering

plate_layout(samples, proj, name_file, save_file_path, starting_plate_number = 1)

7.6.2 tag_layout

param tag_list a dataframe with 3 column : ‘tag_name’ (e.g. f1 to fx and r1 to rx), ‘tag_sequence’ (e.g. ACACACAC) and ‘tag_type’ (i.e. forward or reverse) param PCR_plates a matrix object representing your plates map/layout, output of “plate_layout” function of this package. MAKE SURE that ALL empty cells are filled with NA when importing to R param output_path path to an output folder that will receive to new files param file_corresp_tag name of the sample-tagpairs correspondance dataframe param file_tag_layout name of your xlsx output, having the map of your tagz.

tag_layout(tag_list, PCR_plates, output_path, file_corresp_tag,
    file_tag_layout)