visualizeStereogene {nearBynding} | R Documentation

## visualizeStereogene

### Description

Creates a visual output of a single RNA structure context relative to protein binding.

### Usage

    visualizeStereogene(
      dir_stereogene_output = ".",
      context_file,
      protein_file,
      protein_file_input = NULL,
      x_lim = c(-100, 100),
      y_lim = NULL,
      error = 3,
      nShuffle = 1000,
      out_file = "out_file",
      legend = TRUE,
      heatmap = FALSE
    )

### Arguments

`dir_stereogene_output` | Directory of stereogene output. Default working directory.
`context_file` | A single context file name for visualization with the protein_file(s). File names must exclude extensions such as ".bedGraph". Required.
`protein_file` | A vector of at least one protein file name to be averaged for visualization. File names must exclude extensions such as ".bedGraph". All files in the list should be experimental or biological replicates. Required.
`protein_file_input` | A protein file name of background input to be subtracted from protein_file signal. File name must exclude extension. Only one input file is permitted. Optional.
`x_lim` | A vector of two integers denoting the lower and upper x axis limits. Cannot exceed wSize/2 from write_config. Default (-100, 100)
`y_lim` | A vector of two numbers denoting the lower and upper y axis limits. Optional.
`error` | A numeric value that determines the number of standard deviations to show in the error bar. Default 3
`nShuffle` | Relevant if multiple protein files are input and background error has been calculated. It is the number of iterations used to derive background signal error. Should be same for all protein files. Default 1000.
`out_file` | Name of output file, excluding extension. ".pdf" or ".jpeg" will be added as relevant to the output file name. Default "out_file"
`legend` | Whether a legend should be included with the output graph. Default TRUE.
`heatmap` | Whether the output graph should be in the form of a heatmap (TRUE) or of a line graph (FALSE). Default FALSE

### Value

heatmap (JPEG) or line graph (PDF) image file

### Examples

    ## pull example files
    get_outfiles()
    ## heatmap
    visualizeStereogene(context_file = "chr4and5_3UTR_stem_liftOver",
                       protein_file = "chr4and5_liftOver",
                       out_file = "stem_heatmap",
                       x_lim = c(-500, 500))
    ## line graph
    visualizeStereogene(context_file = "chr4and5_3UTR_stem_liftOver",
                       protein_file = "chr4and5_liftOver",
                       heatmap = TRUE,
                       out_file = "stem_line",
                       x_lim = c(-500, 500))

[Package nearBynding version 1.4.0 Index]