plotLocalizations.Dense-methods: plotLocalizations.Dense
In snjy9182/smt: Single Molecule Tracking

Description Usage Arguments Details Value Examples

Plot localization map of molecules from a list of files in a folder with color coded by local density of each molecule.

1	plotLocalizations.Dense(scale=256,r=125,file.No=0,point.scale=0.15)

`scale`	The pixel scale of image data.
`r`	Radius within each molecule to calculate density.
`file.No`	Select file(s) in the folder to plot. Default 0 for plotting all files in the folder.
`point.scale`	Size of the dots representing the molecules.

Plot localization map of molecules from a list of files in a folder with color coded by local density of each molecule. The localization of molecule is considered as the first position of its track.

Upon running of the function, users will be prompted to input the name of the track list (trackll). Input un-merged trackll and the plotting will start. The local density of each molecule is calculated by counting the number of molecules within a given radius around the position of the molecule. The higher the number, the higher the local density.

PDF: One PDF file with one plot on each page.

# Generate trackll, and process,
# e.g. mask region of interest, tracks from multiple files should not be merged.
folder=system.file("extdata","SWR1",package="smt")
trackll=createTrackll(interact=F,folder,input=1)
trackll=maskTracks(folder,trackll)

# Plot localization map,
plotLocalizations.Dense(scale=256,r=125,file.No=0,point.scale=0.15)