2. Functions overview - shunnnli/NeuroDAP GitHub Wiki

NeuroDAP contains many functions in each major phase of analysis. While some functions requires user to create their own copy for adapting to their specific setup, others are more out of the box and readily usable. Functions in NeuroDAP are listed as follows based on their respective phase of usage.

At the moment, this is not an exhaustive list and functions will be gradually added. Functions with documentation will be denoted as finished.

Recording phase function

• getModPowers()

Preprocessing phase functions

• loadSessions()
• loadSlices()
• concatLabjack() (Create your own)
• demodulateSignal()
• downsampleSignal()
• assignCameraSignals()
• assignChannels()

Session analysis functions

• analyzeSessions() (Create your own)(finished)
• analyzeTraces() (finished)
• getLickBout() (finished)
• getTrials() (finished)
• getTrialTable() (Create your own)(finished)
• getEventTable() (finished)
• getLicks() (finished)
• findTrials() (finished)
• analyzeStages() (finished)
• getLFPWaveforms()
• getModulationIdx()
• getSessionCutoff()
• getSpikes()
• getSpikeWaveforms()
• getSpikeByCluster()
• ranksumSignificance()
• getTraces() (finished)
• getGroupedTrialStats() (finished)
• getRm()

Experiment analysis functions

• concatAnalysis() (finished)
• getAnimalStruct() (finished)
• combineTraces() (finished)
• loadTrialTables() (finished)
• plotSliceEpochs()

Plotting functions

The main goal of plotting functions is to provide essential building blocks for analyze neural signals. Feel free to add your own additional function by combining the following building blocks:

• plotTraces() (finished)
• plotLicks() (finished)
• plotGroupTraces() (finished)
• plotHeatmap() (finished)
• plotEvent() (finished)
• plotSEM() (finished)
• getLegend() (finished)
• initializeFig() (finished)
• saveFigures() (finished)
• loadColors()
• plotSpikes()
• plotSpikeRaster()
• plotSpikeWaveforms()
• plotGroupedTrialStats() (finished)
• plotFFT() (finished)
• plotSignificance() ()
• plotStats() ()

Supplementary functions

These function are supplementary functions that I write based on my workflow. They might be based on established functions in Matlab or functions in Matlab file exchange.

• replaceNaN() (finished)
• findCorrespondingTime() (finished)
• shuffleTraces() (finished)
• osPathSwitch()
• inputAnalysisParams()
• getConsecutive()
• getVarName()
• roundToTarget()
• sortrows_struct()

Low level functions

These function are created and nested in functions described above. You generally don't need to know how they work or use them in your script. They are mostly used in the preprocessing phase during loadSessions()

• assignTimeStamp() (finished)
• getSEM()
• getCI()