plotLocalizations_Density {sojourner} | R Documentation

## plotLocalizations_Density

### Description

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

### Usage

    plotLocalizations_Density(trackll=trackll,scale=256,r=125,file.No=0,
    point.scale=0.15)

### Arguments

`trackll` | trajectory list generated by createTrackll() and processing. if NULL, user will be prompted to enter the trackll name.
`scale` | The pixel scale of image data.
`r` | Radius within each molecule to calculate density in nanometer (nm).
`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.

### Details

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.

### Value

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

### Examples

    # Generate trackll, and process,
    # e.g. mask region of interest, tracks from multiple files should not be
    # merged.
    folder=system.file('extdata','HSF',package='sojourner')
    trackll=createTrackll(folder=folder, input=3)
    trackll=maskTracks(folder,trackll)

    # Plot localization map,
    plotLocalizations_Density(trackll=trackll,scale=128,
                              r=125,file.No=0,point.scale=0.3)
    # Plot only file No. 2 and increase the point size,
    plotLocalizations_Density(trackll=trackll,scale=128,
                              r=125,file.No=2,point.scale=1)

[Package sojourner version 1.8.0 Index]