Package: rda-package
Rhythmic Data AnalysisInclude different functions that allow the user to perform rhythmic data analysis (LS, ARS, JTK, Cosinor, RAIN).InstallationCan be installed withpip:pipinstallrda-packageThen you canimportthe package with :fromrda_packageimportrdaThe setup.cfg file install automatically the dependencies necessary for the proper functioning of the package.Otherwise, if the dependencies do not install automatically, you must manually install them :pipinstallnumpypipinstallpandaspipinstallplotlypipinstallrpy2pipinstallCosinorPypipinstallmatplotlibpipinstallmatplotlib_vennpipinstallseabornpipinstallstatsmodelspipinstallsklearnTo finish, don't forget to install R if it's not already installed :https://cran.r-project.org/bin/windows/base/...and MetaCycle :https://github.com/gangwug/MetaCycle# install 'devtools' in R(>3.0.2)install.packages("devtools")# install MetaCycledevtools::install_github('gangwug/MetaCycle')...and Rain too :https://www.bioconductor.org/packages/release/bioc/html/rain.htmlif(!require("BiocManager",quietly=TRUE))install.packages("BiocManager")BiocManager::install("rain")FunctionscycMouseLiverRNA(filename):
Save MetaCycle dataset cycMouseLiverRNA.cycMouseLiverProtein(filename):Save MetaCycle dataset cycMouseLiverProtein.menetRNASeqMouseLiver(filename):Save RAIN dataset menetRNASeqMouseLiver.meta2d_format(filename,sep=','):Try format a given file to be usable with meta2d.meta2d(filename,filestyle='csv',timepoints='line1',models=["ARS", "JTK", "LS"]):Perform meta2d analysis (JTK, LS and/or, if no replicates, ARS) and store the result in the metaout folder.cosinorpy(filename,sep=',', n_components = [1,2,3], period = 24, folder=None, **kwargs):Perform Cosinor analysis and store the result in the cosinorpyout folder.cosinor1py(filename,sep=',', period = 24,folder=None):Perform 1 component Cosinor analysis and store the result in the cosinorpyout folder.cosinor_pop(filename,sep,period):Perform Cosinor analysis for population data and store the result in the cosinorpyout folder.rain(filename,sample_rate=1,n_replicate=1,period=24):Perform RAIN analysis and store the result in the rainout folder.periodogram(df):Plot the periodogram of a given dataset in cosinor format.plot_meta2d(filename,pvalue_plot=False,amplitude_plot=False,period_plot=False,qvalue_plot=False,phase_plot=False):Plot meta2d result in downloadable graphic table.pv_load(filename):Find all models p-values and save them in one file.pv_dist(filename):Plot and save in images folder p-values distributions.pv_venn(filename):Plot and save in images folder venn diagram using p-values.qv_load(filename):Find all models q-values and save them in one file.qv_dist(filename):Plot and save in images folder q-values distributions.qv_venn(filename):Plot and save in images folder venn diagram using q-values.synt_rhythmic_data(filename,half_rnd=False,n_test=1,n_components=1,noise=0.5,replicates=1):Create test data.  (rhythmic)synt_random_data(filename,n_test=1,replicates=1):Create random test data.  (non-rhythmic)make_metrics(filename,y=None,half_rnd=False,conf_matrix=True,pvalue=False,qvalue=True):Make metrics of an analyzed file.plot_metrics(filename,qvalue=True,pvalue=False):Plot metrics comparaison of ARS,JTK,LS,Meta2d,Cosinor,Rain.file_rda(filename,filestyle='csv',metrics=False,half_rnd=True,n_components=3,replicates=1,sample_rate=2,period=24,y=None,pvalue=False,qvalue=True):Perform meta2d,ARS,JTK,LS,Rain,Cosinor, make pv distribution, venn diagram and can plot metrics.cosinor_read(filename,sep='\t'):Read file in cosinor format, xlsx, csv or txt.export_csv(df,filename):Write a dataframe in a csv in cosinor format.plot_data(df,filename=None):Plot file or dataframe data.cosinor_peaks(df,filename):Plot cosinor peaks of an analysed file.analysis(df,filename,lines='all',dt=None,time_unit_label='hours',T_cutoff = None):pyBOAT signal analysis.plot_detrend(x,y,deg=[1,2,3,5]):Plot detrend ploynomial curve.detrend(x,y,deg):Detrend data.