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], Specifies the transparency of the tree edges. (Default: 1)

line.width:

Numeric scalar. Specifies the default width of an edge. (Default: NULL) to use default of the ggtree package.

line.width.range:

Numeric vector. The range for plotting dynamic edge widths in. (Default: c(0.5,3))

point.alpha:

Numeric scalar in [0, 1]. Specifies the transparency of the tips. (Defaults: 1)

point.size:

Numeric scalar. Specifies the default size of tips. (Defaults: 2.)

point.size.range:

Numeric vector. Specifies the range for plotting dynamic tip sizes in. (Defaults: c(1,4))

label.font.size:

Numeric scalar. Font size for the tip and node labels. (Default: 3)

highlight.font.size:

Numeric scalar. Font size for the highlight labels. (Default: 3)

Graph plotting

line.alpha:

Numeric scalar in [0, 1]. Specifies the transparency of the tree edges. (Default: 1)

line.width:

Numeric scalar. Specifies the default width of an edge. (Default: NULL) to use default of the ggtree package.

line.width.range:

Numeric vector. The range for plotting dynamic edge widths in. (Default: c(0.5,3))

point.alpha:

Numeric scalar in [0, 1]. Specifies the transparency of the tips. (Default: 1)

point.size:

Numeric scalar. Specifies the default size of tips. (Default: 2.)

point.size.range:

Numeric vector. The range for plotting dynamic tip sizes in. (Default: c(1,4))

Abundance plotting

flipped:

Logical scalar. Should the plot be flipped? (Default: FALSE)

add.legend:

Logical scalar. Should legends be plotted? (Default: TRUE)

add.x.text:

Logical scalar. Should x tick labels be plotted? (Default: FALSE)

add.border:

Logical scalar. Should border of bars be plotted? (Default: FALSE)

bar.alpha:

Numeric scalar in [0, 1]. Specifies the transparency of the bars. (Default: 1)

point.alpha:

Numeric scalar in [0, 1]. Specifies the transparency of the points. (Default: 1)

point.size:

Numeric scalar. Specifies the default size of points. (Default: 2.)

Abundance density plotting

add.legend:

Logical scalar. Should legends be plotted? (Defaults: TRUE)

point.shape:

Numeric scalar. Sets the shape of points. (Default: 21)

point.colour:

Character scalar. Specifies the default colour of points. (Default: 2.)

point.size:

Numeric scalar. Specifies the default size of points. (Default: 2.)

point.alpha:

Numeric scalar in [0, 1]. Specifies the transparency of the points. (Default: 1)

flipped:

Logical scalar. Should the plot be flipped? (Default: FALSE)

scales.free:

Logical scalar. Should scales = "free" be set for faceted plots? (Default: TRUE)

angle.x.text:

Logical scalar. Should x tick labels be plotted? (Default: FALSE)

Prevalence plotting

flipped:

Logical scalar. Specifies whether the plot should be flipped. (Default: FALSE)

add.legend:

Logical scalar. Should legends be plotted? (Default: TRUE)

point.alpha:

Numeric scalar in [0, 1]. Specifies the transparency of the tips. (Default: 1)

point.size:

Numeric scalar. Specifies the default size of tips. (Default: 2.)

line.alpha:

Numeric scalar in [0, 1]. Specifies the transparency of the tree edges. (Default: 1)

line.type:

Numeric scalar. Specifies the default line type. (Default: NULL) to use default of the ggplot2 package.

line.size:

Numeric scalar. Specifies the default width of a line. (Default: NULL) to use default of the ggplot2 package.

Series plotting

add.legend:

Logical scalar. Should legends be plotted? (Default: TRUE)

line.alpha:

Numeric scalar in [0, 1]. Specifies the transparency of the tree edges. (Default: 1)

line.type:

Numeric scalar. Specifies the default line type. (Default: NULL) to use default of the ggplot2 package.

line.width:

Numeric scalar. Specifies the default width of a line. (Default: NULL) to use default of the ggplot2 package.

line.width.range:

Numeric vector. The range for plotting dynamic line widths in. (Default: c(0.5,3))

ribbon.alpha:

Numeric scalar in [0, 1]. Specifies the transparency of the ribbon. (Default: 0.3)

Tile plotting

add.legend:

Logical scalar. Should legends be plotted? (Default: TRUE)

rect.alpha:

Numeric scalar in [0, 1]. Specifies the transparency of the areas. (Default: 1)

rect.colour:

Character scalar. Specifies the colour to use for colouring the borders of the areas. (Default: "black")

na.value:

Character scalar. Specifies the colour to use for NA values. (Default: "grey80")

microbiome/miaViz documentation built on Aug. 13, 2024, 8:57 p.m.