transcriptWindow {ORFik} | R Documentation

## Make 100 bases size meta window for all libraries in experiment

### Description

Gives you binned meta coverage plots, either saved seperatly or all in one.

### Usage

    transcriptWindow(
      leaders,
      cds,
      trailers,
      df,
      outdir = NULL,
      scores = c("sum", "transcriptNormalized"),
      allTogether = TRUE,
      colors = experiment.colors(df),
      title = "Coverage metaplot",
      windowSize = min(100, min(widthPerGroup(leaders, FALSE)), min(widthPerGroup(cds,
        FALSE)), min(widthPerGroup(trailers, FALSE))),
      returnPlot = is.null(outdir),
      dfr = NULL,
      idName = "",
      plot.ext = ".pdf",
      type = "ofst",
      is.sorted = FALSE,
      drop.zero.dt = TRUE,
      BPPARAM = bpparam()
    )

### Arguments

`leaders` | a `GRangesList` of leaders (5' UTRs)
`cds` | a `GRangesList` of coding sequences
`trailers` | a `GRangesList` of trailers (3' UTRs)
`df` | an ORFik `experiment`
`outdir` | directory to save to (default: NULL, no saving)
`scores` | scoring function (default: c("sum", "transcriptNormalized")), see ?coverageScorings for possible scores.
`allTogether` | plot all coverage plots in 1 output? (defualt: TRUE)
`colors` | Which colors to use, default auto color from function `experiment.colors`, new color per library type. Else assign colors yourself.
`title` | title of ggplot
`windowSize` | size of binned windows, default: 100
`returnPlot` | return plot from function, default is.null(outdir), so TRUE if outdir is not defined.
`dfr` | an ORFik `experiment` of RNA-seq to normalize against. Will add RNA normalized to plot name if this is done.
`idName` | A character ID to add to saved name of plot, if you make several plots in the same folder, and same experiment, like splitting transcripts in two groups like targets / nontargets etc. (default: "")
`plot.ext` | character, default: ".pdf". Alternatives: ".png" or ".jpg".
`type` | a character(default: "ofst"), load files in experiment or some precomputed variant, either "ofst", "pshifted" or "default". These are made with ORFik:::simpleLibs(), shiftFootprintsByExperiment().. Will load default if bedoc is not found
`is.sorted` | logical (FALSE), is grl sorted. That is + strand groups in increasing ranges (1,2,3), and - strand groups in decreasing ranges (3,2,1)
`drop.zero.dt` | logical FALSE, if TRUE and as.data.table is TRUE, remove all 0 count positions. This greatly speeds up and most importantly, greatly reduces memory usage. Will not change any plots, unless 0 positions are used in some sense. (mean, median, zscore coverage will only scale differently)
`BPPARAM` | how many cores/threads to use? default: bpparam()

### Value

NULL, or ggplot object if returnPlot is TRUE

### See Also

Other experiment plots: `transcriptWindow1()`, `transcriptWindowPer()`

### Examples

    df <- ORFik.template.experiment()[3,] # Only third library
    loadRegions(df) # Load leader, cds and trailers as GRangesList
    #transcriptWindow(leaders, cds, trailers, df, outdir = "directory/to/save")

[Package ORFik version 1.14.7 Index]