mia-plot-args: Additional arguments for plotting

In microbiome/miaViz: Microbiome Analysis Plotting and Visualization

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, specifying the colour to use for colouring the borders of the areas. Defaults to "black".

na.value:

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

microbiome/miaViz documentation built on April 21, 2024, 8:45 a.m.