ScatterView {MAGeCKFlute} | R Documentation

## Scatter plot

### Description

Scatter plot supporting groups.

### Usage

    ScatterView(
      data,
      x = "x",
      y = "y",
      label = 0,
      model = c("none", "ninesquare", "volcano", "rank")[1],
      x_cut = NULL,
      y_cut = NULL,
      slope = 1,
      intercept = NULL,
      auto_cut = FALSE,
      auto_cut_x = auto_cut,
      auto_cut_y = auto_cut,
      auto_cut_diag = auto_cut,
      groups = NULL,
      group_col = NULL,
      groupnames = NULL,
      label.top = TRUE,
      top = 0,
      toplabels = NULL,
      display_cut = FALSE,
      color = NULL,
      shape = 16,
      size = 1,
      alpha = 0.6,
      main = NULL,
      xlab = x,
      ylab = y,
      legend.position = "none",
      ...
    )

### Arguments

`data` | Data frame.
`x` | A character, specifying the x-axis.
`y` | A character, specifying the y-axis.
`label` | An integer or a character specifying the column used as the label, default value is 0 (row names).
`model` | One of "none" (default), "ninesquare", "volcano", and "rank".
`x_cut` | An one or two-length numeric vector, specifying the cutoff used for x-axis.
`y_cut` | An one or two-length numeric vector, specifying the cutoff used for y-axis.
`slope` | A numberic value indicating slope of the diagonal cutoff.
`intercept` | A numberic value indicating intercept of the diagonal cutoff.
`auto_cut` | Boolean, take 1.5 fold standard deviation as cutoff.
`auto_cut_x` | Boolean, take 1.5 fold standard deviation as cutoff on x-axis.
`auto_cut_y` | Boolean, take 1.5 fold standard deviation as cutoff on y-axis.
`auto_cut_diag` | Boolean, take 1.5 fold standard deviation as cutoff on diagonal.
`groups` | A character vector specifying groups. Optional groups include "top", "mid", "bottom", "left", "center", "right", "topleft", "topcenter", "topright", "midleft", "midcenter", "midright", "bottomleft", "bottomcenter", "bottomright".
`group_col` | A vector of colors for specified groups.
`groupnames` | A vector of group names to show on the legend.
`label.top` | Boolean, specifying whether label top hits.
`top` | Integer, specifying the number of top terms in the groups to be labeled.
`toplabels` | Character vector, specifying terms to be labeled.
`display_cut` | Boolean, indicating whether display the dashed line of cutoffs.
`color` | A character, specifying the column name of color in the data frame.
`shape` | A character, specifying the column name of shape in the data frame.
`size` | A character, specifying the column name of size in the data frame.
`alpha` | A numeric, specifying the transparency of the dots.
`main` | Title of the figure.
`xlab` | Title of x-axis
`ylab` | Title of y-axis.
`legend.position` | Position of legend, "none", "right", "top", "bottom", or a two-length vector indicating the position.
`...` | Other available parameters in function 'geom_text_repel'.

### Value

An object created by `ggplot`, which can be assigned and further customized.

### Author(s)

Wubing Zhang

### Examples

    file3 = file.path(system.file("extdata", package = "MAGeCKFlute"),
    "testdata/mle.gene_summary.txt")
    dd = ReadBeta(file3)
    ScatterView(dd, x = "dmso", y = "plx", label = "Gene",
    x_cut = 1, y_cut = 1, groups = "topright", top = 5, display_cut = TRUE)

[Package MAGeCKFlute version 1.12.0 Index]