create_raw_summary_array: Create the raw summary array for all spikes

In sfrechter/physplit.analysis: Packaged and versioned Analysis functions for Shahar's cells

Description

create_simple_summary_array creates a matrix containing every 7 time point summarised from the smooth psth.

create_simple_summary_array creates a list of matrices, one for each cell, containing every time point in the smoothed PSTH (rows) x every possible odour (cols).

Usage

create_raw_summary_array(x = physplitdata::smSpikes, cells = NULL)

create_simple_summary_arrays(x = physplitdata::smSpikes, cells = NULL)

Arguments

x	A list of smoothed psth objects for cell/odours combinations. Defaults to smSpikes
cells	A character vector of cell names enabling calculation of summary_array for a subset of the data.

See Also

Other summary_array: createSummarySpikesMat

Examples

summary_array=create_raw_summary_array()
# histogram of baseline firing for all cells / odours
hist(summary_array[,,'baseline'])
# collapse all data for different odours for the same cell
# i.e. average baseline firing rate for each cell
baseline_cell=rowMeans(summary_array[,,'baseline'], na.rm=TRUE)
hist(baseline_cell, xlab='Firing freq /Hz')

# examples of calculating summary for all cells
summary_array3=create_raw_summary_array(cells=c("nm20140714c1", "nm20150305c0", "nm20141128c0"))

# Plot density distributions by cell group
pns=subset(PhySplitDB, Group=='PN' & cell %in% names(smSpikes))$cell
physplit=PhySplitDB[match(names(smSpikes), PhySplitDB$cell), ]
rownames(physplit)=physplit$cell
physplit$baseline=baseline_cell[physplit$cell]
library(ggplot2)
qplot(baseline,col=Group, data=subset(physplit, Group%in%c("L","O","PN")), geom='density')

sfrechter/physplit.analysis documentation built on May 29, 2019, 8:02 p.m.