ssvSignalScatterplot {seqsetvis} | R Documentation

## maps signal from 2 sample profiles to the x and y axis. axes are standard or "volcano" min XY vs fold-change Y/X

### Description

maps signal from 2 sample profiles to the x and y axis. axes are standard or "volcano" min XY vs fold-change Y/X

### Usage

    ssvSignalScatterplot(
      bw_data,
      x_name,
      y_name,
      color_table = NULL,
      value_variable = "y",
      xy_variable = "sample",
      value_function = max,
      by_ = "id",
      plot_type = c("standard", "volcano")[1],
      show_help = FALSE,
      fixed_coords = TRUE,
      return_data = FALSE
    )

### Arguments

`bw_data` | a GRanges or data.table of bigwig signal. As returned from `ssvFetchBam` and `ssvFetchBigwig`
`x_name` | sample name to map to x-axis, must be stored in variable specified in `xy_variable`
`y_name` | sample name to map to y-axis, must be stored in variable specified in `xy_variable`
`color_table` | data.frame with 2 columns, one of which must be named "group" and gets mapped to color. The other column must be the same as by_ parameter and is used for merging.
`value_variable` | variable name that stores numeric values for plotting, default is "y"
`xy_variable` | variable name that stores sample, must contain entires for `x_name` and `y_name`
`value_function` | a function to apply to `value_variable` in all combintations of `by_` per `x_name` and `y_name`
`by_` | variables that store individual measurement ids
`plot_type` | standard or volcano, default is "standard"
`show_help` | if TRUE overlay labels to aid plot interpretation, default is FALSE
`fixed_coords` | if TRUE coordinate system is 1:1 ratio, default is TRUE
`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 points comparing signal from 2 samples

### Examples

    ssvSignalScatterplot(CTCF_in_10a_profiles_gr,
        x_name = "MCF10A_CTCF", y_name = "MCF10AT1_CTCF")
    ssvSignalScatterplot(CTCF_in_10a_profiles_gr,
        x_name = "MCF10A_CTCF", y_name = "MCF10CA1_CTCF")

    ssvSignalScatterplot(CTCF_in_10a_profiles_gr,
        x_name = "MCF10A_CTCF", y_name = "MCF10AT1_CTCF",
        value_function = median) + labs(title = "median FE in regions")

    ssvSignalScatterplot(CTCF_in_10a_profiles_gr,
        x_name = "MCF10A_CTCF", y_name = "MCF10AT1_CTCF",
        plot_type = "volcano")

    ssvSignalScatterplot(CTCF_in_10a_profiles_gr,
        x_name = "MCF10A_CTCF", y_name = "MCF10AT1_CTCF",
        plot_type = "volcano", show_help = TRUE)

[Package seqsetvis version 1.12.0 Index]