mia-plot-args {miaViz} | R Documentation

## Additional arguments for plotting

### Description

To be able to fine tune plotting, several additional plotting arguments are available. These are described on this page.

### Tree plotting

`line_alpha`:

  Numeric scalar in `[0, 1]`, specifying the transparency of the tree edges. Defaults to `1`.

`line_width`:

  Numeric scalar, specifying the default width of an edge. Defaults to NULL to use default of the `ggtree` package

`line_width_range`:

  Two numeric values, the range for plotting dynamic edge widths in. Defaults to `c(0.5,3)`.

`point_alpha`:

  Numeric scalar in `[0, 1]`, specifying the transparency of the tips. Defaults to `1`.

`point_size`:

  Numeric scalar, specifying the default size of tips Defaults to `2.`.

`point_size_range`:

  Two numeric values, the range for plotting dynamic tip sizes in. Defaults to `c(1,4)`.

`label_font_size`:

  Numeric scalar, font size for the tip and node labels. Default to `3`.

`highlight_font_size`:

  Numeric scalar, font size for the highlight labels. Default to `3`.

### Graph plotting

`line_alpha`:

  Numeric scalar in `[0, 1]`, specifying the transparency of the tree edges. Defaults to `1`.

`line_width`:

  Numeric scalar, specifying the default width of an edge. Defaults to NULL to use default of the `ggraph` package

`line_width_range`:

  Two numeric values, the range for plotting dynamic edge widths in. Defaults to `c(0.5,3)`.

`point_alpha`:

  Numeric scalar in `[0, 1]`, specifying the transparency of the tips. Defaults to `1`.

`point_size`:

  Numeric scalar, specifying the default size of tips Defaults to `2.`.

`point_size_range`:

  Two numeric values, the range for plotting dynamic tip sizes in. Defaults to `c(1,4)`.

### Abundance plotting

`flipped`:

  Logical scalar. Should the plot be flipped? Defaults to `FALSE`.

`add_legend`:

  Logical scalar. Should legends be plotted? Defaults to `TRUE`.

`add_x_text`:

  Logical scalar. Should x tick labels be plotted? Defaults to `FALSE`.

`add_border`:

  Logical scalar. Should border of bars be plotted? Defaults to `FALSE`.

`bar_alpha`:

  Numeric scalar in `[0, 1]`, specifying the transparency of the bars. Defaults to `1`.

`point_alpha`:

  Numeric scalar in `[0, 1]`, specifying the transparency of the points. Defaults to `1`.

`point_size`:

  Numeric scalar, specifying the default size of points. Defaults to `2.`.

### Abundance density plotting

`add_legend`:

  Logical scalar. Should legends be plotted? Defaults to `TRUE`.

`point_shape`:

  Numeric scalar setting the shape of points. Defaults to `21`.

`point_colour`:

  Character scalar, specifying the default colour of points. Defaults to `2.`.

`point_size`:

  Numeric scalar, specifying the default size of points. Defaults to `2.`.

`point_alpha`:

  Numeric scalar in `[0, 1]`, specifying the transparency of the points. Defaults to `1`.

`flipped`:

  Logical scalar. Should the plot be flipped? Defaults to `FALSE`.

`scales_free`:

  Logical scalar. Should `scales = "free"` be set for faceted plots? Defaults to `TRUE`.

`angle_x_text`:

  Logical scalar. Should x tick labels be plotted? Defaults to `FALSE`.

### Prevalence plotting

`flipped`:

  Logical scalar, specifying whether the plot should be flipped. Defaults to `FALSE`.

`add_legend`:

  Logical scalar. Should legends be plotted? Defaults to `TRUE`.

`point_alpha`:

  Numeric scalar in `[0, 1]`, specifying the transparency of the tips. Defaults to `1`.

`point_size`:

  Numeric scalar, specifying the default size of tips Defaults to `2.`.

`line_alpha`:

  Numeric scalar in `[0, 1]`, specifying the transparency of the tree edges. Defaults to `1`.

`line_type`:

  Numeric scalar, specifying the default line type. Defaults to NULL to use default of the `ggplot2` package

`line_size`:

  Numeric scalar, specifying the default width of a line. Defaults to NULL to use default of the `ggplot2` package

### Series plotting

`add_legend`:

  Logical scalar. Should legends be plotted? Defaults to `TRUE`.

`line_alpha`:

  Numeric scalar in `[0, 1]`, specifying the transparency of the tree edges. Defaults to `1`.

`line_type`:

  Numeric scalar, specifying the default line type. Defaults to NULL to use default of the `ggplot2` package

`line_width`:

  Numeric scalar, specifying the default width of a line. Defaults to NULL to use default of the `ggplot2` package

`line_width_range`:

  Two numeric values, the range for plotting dynamic line widths in. Defaults to `c(0.5,3)`.

`ribbon_alpha`:

  Numeric scalar in `[0, 1]`, specifying the transparency of the ribbon. Defaults to `0.3`.

### Tile plotting

`add_legend`:

  Logical scalar. Should legends be plotted? Defaults to `TRUE`.

`rect_alpha`:

  Numeric scalar in `[0, 1]`, specifying the transparency of the areas. Defaults to `1`.

`rect_colour`:

  Character scalar, specfiying the colour to use for colouring the borders of the areas. Defaults to `"black"`.

`na.value`:

  Character scalar, specfiying the colour to use for `NA` values. Defaults to `"grey80"`.

[Package miaViz version 1.2.1 Index]