meaRtools: generate.raster.plot – R documentation

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generate.raster.plot

generate_raster_plot

Description

Creates a pdf raster plot of selected user selected well from an 's' object. Options include verticle lines showing network spike times, vertical bars showing bursts as well as # showing count of spikes in burst and network spikes.

Usage

generate_raster_plot(r_object_file = NULL, outputdir = NULL, well_for_raster
                 = NULL, interval_for_raster = NULL, show_bursts = F,
                 show_burst_number = F, show_networkspikes = F,
                 show_ns_number = F,  show_nb=F, window_size=NULL)

Arguments

`r_object_file`	Default value is NULL, in which case tcltk pop-up file chooser will prompt user to select an 's' object. Otherwise, provide a full path to to a .RData 's' object that contains burst and network data.
`outputdir`	A directory (character string in quotes) where pdf is to be saved. Default is NULL, in which case the plot will be saved in the directory r_object_file location.
`well_for_raster`	A well name, character string, from plate. e.g. well_for_raster="A3". Default is NULL, in which case first well in plate will appear in plot.
`interval_for_raster`	A vector of min and max time (s) for raster marks. e.g. interval_for_raster=c(30,60) Default is NULL, in which case the whole recording interval will be used.
`show_bursts`	A boolean value sets whether bursts are indicated by red horizontal line (TRUE/FALSE) e.g. show_bursts=FALSE Default=FALSE
`show_burst_number`	A boolean value sets whether # spikes/bursts are indicated (TRUE/FALSE). show_bursts must be set to true in order that show_burst_number=T e.g. show_burst_number=FALSE Default=FALSE
`show_networkspikes`	A boolean value sets whether network spikes are indicated by green vertical line (TRUE/FALSE) e.g. show_networkspikes=FALSE Default=FALSE
`show_ns_number`	A boolean value sets whether # electrodes in network spikes are indicated (TRUE/FALSE) e.g. show_ns_number=FALSE Default=FALSE
`show_nb`	A boolean value sets whether network bursts should be indicated in raster by orange horizontal lines (TRUE/FALSE) e.g. show_ns_number=FALSE Default=FALSE
`window_size`	A numeric value indicating which of the three smoothing sizes available in the R-object should be used in network burst identification e.g. show_ns_number=10Default=NULL

Value

A pdf raster plot will be displayed in system viewer.

Author(s)

Diana Hall

Examples

generate_raster_plot(r_object_file=NULL,
                      well_for_raster=NULL, 
                      interval_for_raster=NULL,
                      show_bursts=F, 
                      show_burst_number=F, 
                      show_networkspikes=F,
                      show_ns_number=F,
                      show_nb=F,
                      window_size=NULL )

meaRtools

Micro-Electro Array (MEA) Analysis

v1.0.4

GPL (>= 3)

Authors

Quanli Wang [aut, ctb], Sahar Gelfman [aut, ctb, cre], Diana Hall [aut, ctb], Ryan Dhindsa [aut, ctb], Matt Halvorsen [aut, ctb], Ellese Cotterill [aut, ctb], Tom Edinburgh [aut, ctb], Stephen J. Eglen [aut, ctb, ths]

Initial release

2018-7-1