coverageHeatMap {ORFik} | R Documentation

## Create a heatmap of coverage

### Description

Creates a ggplot representing a heatmap of coverage:

- Rows : Position in region

- Columns : Read length

- Index intensity : (color) coverage scoring per index.

Coverage rows in heat map is fraction, usually fractions is divided into unique read lengths (standard Illumina is 76 unique widths, with some minimum cutoff like 15.) Coverage column in heat map is score, default zscore of counts. These are the relative positions you are plotting to. Like +/- relative to TIS or TSS.

### Usage

    coverageHeatMap(
      coverage,
      output = NULL,
      scoring = "zscore",
      legendPos = "right",
      addFracPlot = FALSE,
      xlab = "Position relative to start site",
      ylab = "Protected fragment length",
      colors = "default",
      title = NULL,
      increments.y = "auto",
      gradient.max = max(coverage$score)
    )

### Arguments

`coverage` | a data.table, e.g. output of scaledWindowCoverage
`output` | character string (NULL), if set, saves the plot as pdf or png to path given. If no format is given, is save as pdf.
`scoring` | character vector, default "zscore", Which scoring did you use to create? either of zscore, transcriptNormalized, sum, mean, median, .. see ?coverageScorings for info and more alternatives.
`legendPos` | a character, Default "right". Where should the fill legend be ? ("top", "bottom", "right", "left")
`addFracPlot` | Add margin histogram plot on top of heatmap with fractions per positions
`xlab` | the x-axis label, default "Position relative to start site"
`ylab` | the y-axis label, default "Protected fragment length"
`colors` | character vector, default: "default", this gives you: c("white", "yellow2", "yellow3", "lightblue", "blue", "navy"), do "high" for more high contrasts, or specify your own colors.
`title` | a character, default NULL (no title), what is the top title of plot?
`increments.y` | increments of y axis, default "auto". Or a numeric value < max position & > min position.
`gradient.max` | numeric, defualt: max(coverage$score). What data value should the top color be ? Good to use if you want to compare 2 samples, with the same color intensity, in that case set this value to the max score of the 2 coverage tables.

### Details

Colors: Remember if you want to change anything like colors, just return the ggplot object, and reassign like: obj + scale_color_brewer() etc. Standard colors are:

- 0 reads in whole readlength :gray

- few reads in position :white

- medium reads in position :yellow

- many reads in position :dark blue

### Value

a ggplot object of the coverage plot, NULL if output is set, then the plot will only be saved to location.

### See Also

Other heatmaps: `heatMapL()`, `heatMapRegion()`, `heatMap_single()`

Other coveragePlot: `pSitePlot()`, `savePlot()`, `windowCoveragePlot()`

### Examples

    # An ORF
    grl <- GRangesList(tx1 = GRanges("1", IRanges(1, 6), "+"))
    # Ribo-seq reads
    range <- IRanges(c(rep(1, 3), 2, 3, rep(4, 2), 5, 6), width = 1 )
    reads <- GRanges("1", range, "+")
    reads$size <- c(rep(28, 5), rep(29, 4)) # read size
    coverage <- windowPerReadLength(grl, reads = reads, upstream = 0,
                                    downstream = 5)

    coverageHeatMap(coverage)

    # With top sum bar
    coverageHeatMap(coverage, addFracPlot = TRUE)
    # See vignette for more examples

[Package ORFik version 1.12.13 Index]