ssvSignalBandedQuantiles {seqsetvis} | R Documentation

## plot profiles from bigwigs

### Description

plot profiles from bigwigs

### Usage

    ssvSignalBandedQuantiles(
      bw_data,
      y_ = "y",
      x_ = "x",
      by_ = "fake",
      hsv_reverse = FALSE,
      hsv_saturation = 1,
      hsv_value = 1,
      hsv_grayscale = FALSE,
      hsv_hue_min = 0,
      hsv_hue_max = 0.7,
      hsv_symmetric = FALSE,
      n_quantile = 18,
      quantile_min = 0.05,
      quantile_max = 0.95,
      return_data = FALSE
    )

### Arguments

`bw_data` | a GRanges or data.table of bigwig signal. As returned from `ssvFetchBam` and `ssvFetchBigwig`
`y_` | the variable name in bw_data for y axis in plot
`x_` | the variable name in bw_data for x axis in plot
`by_` | the variable name in bw_data to facet on
`hsv_reverse` | logical, should color scale be reversed? default FALSE
`hsv_saturation` | numeric [0, 1] saturation for color scale. default 1
`hsv_value` | numeric [0, 1] value for color scale. default 1
`hsv_grayscale` | logical, if TRUE gray() is used instead of rainbow(). default FALSE
`hsv_hue_min` | numeric [0, hsv_hue_max) hue min of color scale
`hsv_hue_max` | numeric (hsv_hue_min, 1] hue max of color scale
`hsv_symmetric` | if TRUE, colorscale is symmetrical, default FALSE.
`n_quantile` | number of evenly size quantile bins
`quantile_min` | the lowest quantile start
`quantile_max` | the highest quantile end
`return_data` | logical. If TRUE, return value is no longer ggplot and is instead the data used to generate that plot. Default is FALSE.

### Value

ggplot object using ribbon plots to show quantile distributions

### Examples

    #rainbow colors
    qgr = CTCF_in_10a_profiles_gr
    ssvSignalBandedQuantiles(qgr)
    #grayscale
    ssvSignalBandedQuantiles(qgr, hsv_grayscale = TRUE,
        hsv_symmetric = TRUE, hsv_reverse = TRUE)
    #using "by_" per sample
    ssvSignalBandedQuantiles(qgr, hsv_grayscale = TRUE,
        hsv_symmetric = TRUE, hsv_reverse = TRUE, by_ = "sample")
    #adding spline smoothing
    splined = applySpline(qgr, n = 10,
        by_ = c("id", "sample"))
    ssvSignalBandedQuantiles(splined, n_quantile = 50,
        quantile_min = .25, quantile_max = .75,
        hsv_symmetric = TRUE, hsv_reverse = TRUE, by_ = "sample")

[Package seqsetvis version 1.12.0 Index]