SpatialProperties2d-class: A S4 class to analyze spatial properties in 2D environments
In kevin-allen/relectro: Analysis of electrophysiological data

Description Slots

Use to get firing rate maps of neurons in an open field. It can get information scores, sparsity, etc. You can use it to analyze the firing properties of grid cells or border cells. Can do some shuffling to get the spatial properties that you would get by chance.

session: Name of the recording session
cmPerBin: Number of cm in each bin of a firing rate map, 2 by default
smoothOccupancySd: Standard deviation in cm of the gaussian kernel used to smooth the occupancy map, 3 by default
smoothRateMapSd: Standard deviation in cm of the gaussian kernel used to smooth the firing rate histograms, 3 by default
nColMap: Number of columns in the firing rate maps
nRowMap: Number of rows in the firing rate maps
nColAuto: Number of columns in the spatial autocorrelation
nRowAuto: Number of rows in the spatial autocorrelation
nColCross: Number of columns in the spatial crosscorrelation
nRowCross: Number of rows in the spatial crosscorrelation
xSpikes: x position of the animal for each spike time
ySpikes: y position of the animal for each spike time
maps: Array containing the firing rate maps of the neurons
ccMaps: Array containing the crosscorrelation of firing rate maps
occupancy: Matrix containing the occupancy map
occupancy3D: Array containing the occupancy for x and y positions and head-direction.
autos: Array containing the spatial autocorrelation of the firing rate maps
autosDetect: Array with the spatial autocorrelation once the firing fields have been removed
autosDoughnut: Array with the spatial autocorrelation containing only the ring of the 6 closest fields (excluding central field)
autosDoughnutRotate: Array with the rotated spatial autocorrelations
cellList: List of cells
cellPairList: List of cell pairs
reduceSize: Logical indicating if the size of map should be minimized by setting smallest x and y to 0
minValidBinsAuto: Number of valid bins to calculate a r value in the spatial autocorrelation maps
minValidBinsCross: Number of valid bins to calculate a r value in the spatial crosscorrelation maps
peakRate: Peak firing rates in the maps
infoScore: Information score of the firing rate maps
sparsity: Sparsity of the firing rate maps
borderScore: Border score for each firing rate maps
borderCM: Value of CM when calculating the border score
borderDM: Value of DM when calculating the border score
borderNumFieldsDetected: Number of detected fields when calculating the border score
borderPercentageThresholdField: Threshold for a bin being part of a field, expressed as percentage of peak
borderMinBinsInField: Minimum number of bins to be considered a field
mapPolarity: How polarized is the firing rate of the cell in the map. Each bin of the map is given an angle and firing rate. mapPolarity is the resultant mean vector length
gridScore: Grid score calculated form the spatial autocorrelation
gridOrientation: Grid orientation
gridSpacing: Grid spacing in cm
gridScoreNumberFieldsToDetect: Maximal number of fields that will be detected
gridScoreMinNumBinsPerField: Minimum number of bins to be considered a field
gridScoreFieldThreshold: Minimum value of firing fields in the spatial autocorrelation map
nAutoRotations: Number of rotations when rotating the spatial autocorrelation map
AutoRotationDegree: Angle of rotation of the spatial autocorrelation map
speedScore: Speed score of the neurons
speedRateSlope: Slope of the linear regression line between speed and rate
speedRateIntercept: Rate intercept of the linear regression line between speed and rate
nShufflings: Number of shufflings to get chance levels, by default 100
minShiftMs: Minimum time shift of the position data when doing shuffling
peakRateShuffle: peak firing rate in the shuffling analysis
infoScoreShuffle: Information score from the shuffling analysis
sparsityShuffle: Sparsity from the shuffling analysis
borderScoreShuffle: Border score form the shuffling analysis
borderCMShuffle: Border CM from the shuffling analysis
borderDMShuffle: Border DM from the shuffling analysis
borderNumFieldsDetectedShuffle: Number of detected fields when calculating shufflings of the border score
mapPolarityShuffle: Map polarity from the shuffling analysis
gridScoreShuffle: Grid score from the shuffling analysis
speedScoreShuffle: Speed score from the shuffling analysis