plotAnansi: miaViz style plotting wrapper for anansi output

In thomazbastiaanssen/anansi: Annotation-Based Analysis of Specific Interactions

miaViz style plotting wrapper for anansi output

Description

plotAnansi generates a standard dissociation plot from the output of getAnansi() in the table format. It provides a convenient way to visually assess relevant results from the anansi analysis.

Usage

plotAnansi(x, ...)

plotAnansi(x, ...)

## S4 method for signature 'data.frame'
plotAnansi(
  x,
  association.type = NULL,
  model.var = NULL,
  signif.threshold = NULL,
  colour_by = NULL,
  color_by = colour_by,
  fill_by = "group",
  size_by = NULL,
  shape_by = NULL,
  y_position = "right",
  x_lab = "cor",
  y_lab = ""
)

Arguments

x	a data.frame object output of getAnansi() in the table format.
...	additional arguments
association.type	⁠Character scalar⁠. Specifies the type of association to show in the plot. One of "disjointed", "emergent" and "full". (Default: NULL)
model.var	⁠Character scalar⁠. Specifies the name of a variable in the anansi model. It is relevant only when association.type is "disjointed" or "emergent". (Default: NULL)
signif.threshold	⁠Numeric scalar⁠. Specifies the threshold to mark the significance of association.type. (Default: NULL)
colour_by	⁠Character scalar⁠. Specifies one of the groups terms used in the original anansi call, x by which points should be coloured. (Default: NULL)
color_by	⁠Character scalar⁠. Alias to colour_by.
fill_by	⁠Character scalar⁠. Specifies one of the groups terms used in the original anansi call, x by which points should be filled (Default: "group")
size_by	⁠Character scalar⁠. Specifies one of the groups terms used in the original anansi call, x by which points should be sized. (Default: NULL)
shape_by	⁠Character scalar⁠. Specifies one of the groups terms used in the original anansi call, x by which points should be shaped. (Default: NULL)
y_position	⁠Character scalar⁠. Specifies the position of the y labels. It should be either "left" or "right". (Default: "right")
x_lab	⁠Character scalar⁠. Specifies the label of the x axis. (Default: "cor")
y_lab	⁠Character scalar⁠. Specifies the label of the y axis. (Default: "")

Details

plotAnansi provides a standardised method to visualise the results of anansi by means of a differential association plot. The input for this function should be generated from getAnansi() or anansi(), with return.format = "table"

Value

A ggplot2 object.

See Also

getAnansi() anansi()

Examples

# Import libraries
library(mia)
library(TreeSummarizedExperiment)
library(MultiAssayExperiment)

web <- randomWeb(n_samples = 100)
mae <- as(web, "MultiAssayExperiment")

# Perform anansi analysis
out <- getAnansi(mae,
    tableY = "y", tableX = "x",
    formula = ~group_ab
)

# Select significant interactions
out <- out[out$full_p.values < 0.05, ]

# Visualise disjointed associations filled by group
plotAnansi(out,
    association.type = "disjointed",
    model.var = "group_ab",
    signif.threshold = 0.05,
    fill_by = "group"
)

# Visualise full associations filled by group
plotAnansi(out,
    association.type = "full",
    signif.threshold = 0.05,
    fill_by = "group"
)

thomazbastiaanssen/anansi documentation built on June 9, 2025, 3:59 p.m.