ssvSignalLineplot {seqsetvis} | R Documentation

## construct line type plots where each region in each sample is represented

### Description

construct line type plots where each region in each sample is represented

### Usage

    ssvSignalLineplot(
      bw_data,
      x_ = "x",
      y_ = "y",
      color_ = "sample",
      sample_ = "sample",
      region_ = "id",
      group_ = "auto_grp",
      line_alpha = 1,
      facet_ = "auto_facet",
      facet_method = facet_wrap,
      spline_n = NULL,
      return_data = FALSE
    )

### Arguments

`bw_data` | a GRanges or data.table of bigwig signal. As returned from `ssvFetchBam` and `ssvFetchBigwig`
`x_` | variable name mapped to x aesthetic, x by default.
`y_` | variable name mapped to y aesthetic, y by default.
`color_` | variable name mapped to color aesthetic, sample by default.
`sample_` | variable name, along with region_ used to group and facet by default, change group_ or facet_ to override.
`region_` | variable name, along with sample_ used to group and facet by default, change group_ or facet_ to override.
`group_` | group aesthetic keeps lines of geom_path from mis-connecting. auto_grp by default which combines sample_ and region_. probably shouldn't change.
`line_alpha` | alpha value for lines. default is 1.
`facet_` | facetting divides up plots. auto_facet by default which combines sample_ and region_. if overriding facet_method with facet_grid, make sure to include ~ between two variables, ie. "a~b", ".~b", "a~."
`facet_method` | ggplot2 facetting method or wrapper for same, facet_wrap by default.
`spline_n` | if not NULL, applySpline will be called with n = spline_n. default is NULL.
`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 of signal potentially facetted by region and sample

### Examples

    bw_gr = CTCF_in_10a_profiles_gr
    ssvSignalLineplot(subset(bw_gr, bw_gr$id %in% seq_len(3)), facet_ = "sample")
    ssvSignalLineplot(subset(bw_gr, bw_gr$id %in% seq_len(3)),
        facet_ = "sample~.",
        facet_method = facet_grid)
    ssvSignalLineplot(subset(bw_gr, bw_gr$id %in% seq_len(3)),
        facet_ = paste("sample", "~", "id"), facet_method = facet_grid)
    ssvSignalLineplot(subset(bw_gr, bw_gr$id %in% seq_len(3)))
    ssvSignalLineplot(subset(bw_gr, bw_gr$id %in% seq_len(3)), facet_ = "id")
    ssvSignalLineplot(subset(bw_gr, bw_gr$id %in% seq_len(3)),
        facet_ = "id", spline_n = 10)

[Package seqsetvis version 1.14.4 Index]