PathwaySpace (version 1.1.1)

plotPathwaySpace,PathwaySpace-method: Plotting 2D-landscape images for the PathwaySpace package

Description

plotPathwaySpace is a wrapper function to create dedicated ggplot graphics for PathwaySpace-class objects.

Usage

# S4 method for PathwaySpace
plotPathwaySpace(
  ps,
  colors = pspace.cols(),
  bg.color = "grey95",
  si.color = "grey85",
  si.alpha = 1,
  theme = c("th0", "th1", "th2", "th3"),
  title = "PathwaySpace",
  xlab = "Pathway coordinates 1",
  ylab = "Pathway coordinates 2",
  zlab = "Density",
  font.size = 1,
  font.color = "white",
  zlim = NULL,
  slices = 25,
  add.grid = TRUE,
  grid.color = "white",
  add.summits = TRUE,
  label.summits = TRUE,
  summit.color = "white",
  add.marks = FALSE,
  marks = NULL,
  mark.size = 3,
  mark.color = "white",
  mark.padding = 0.5,
  mark.line.width = 0.5,
  use.dotmark = FALSE,
  add.image = FALSE
)

Value

A ggplot-class object.

Arguments

ps

A PathwaySpace class object.

colors

A vector of colors.

bg.color

A single color for background.

si.color

A single color for silhouette. (see silhouetteMapping).

si.alpha

A transparency level in [0, 1], used to adjust the opacity of the silhouette. This parameter is useful for improving the perception of a background image, when one is available.

theme

Name of a custom PathwaySpace theme. These themes (from 'th0' to 'th3') consist mainly of preconfigured ggplot settings, which the user can subsequently refine using ggplot2.

title

A string for the title.

xlab

The title for the 'x' axis of a 2D-image space.

ylab

The title for the 'y' axis of a 2D-image space.

zlab

The title for the 'z' axis of the image signal.

font.size

A single numeric value passed to plot annotations.

font.color

A single color passed to plot annotations.

zlim

The 'z' limits of the plot (a numeric vector with two numbers). If NULL, limits are determined from the range of the input values.

slices

A single positive integer value used to split the image signal into equally-spaced intervals.

add.grid

A logical value indicating whether to add gridlines to the image space. However, gridlines will only appear when the image is decorated with graph silhouettes (see silhouetteMapping).

grid.color

A color passed to geom_point.

add.summits

A logical value indicating whether to add contour lines to 'summits' (when summits are available; see summitMapping).

label.summits

A logical value indicating whether to label summits.

summit.color

A color passed to 'summits'.

add.marks

A logical value indicating whether to plot vertex labels.

marks

A vector of vertex names to be highlighted in the image space. This argument overrides 'add.labels'.

mark.size

A size argument passed to geom_text.

mark.color

A color passed to geom_text.

mark.padding

A box padding argument passed to geom_text_repel.

mark.line.width

A line width argument passed to geom_text_repel.

use.dotmark

A logical value indicating whether "marks" should be represented as dots.

add.image

A logical value indicating whether to add a background image, when one is available (see GraphSpace).

Author

Sysbiolab Team, Mauro Castro.

See Also

circularProjection

Examples

# Load a demo igraph
data('gtoy1', package = 'RGraphSpace')

# # Check graph validity
gs <- GraphSpace(gtoy1)

# Create a PathwaySpace object
ps <- buildPathwaySpace(gs, nrc = 300)
# note: adjust 'nrc' to increase image resolution

# Set '1s' as vertex signal
vertexSignal(ps) <- 1

# Create a 2D-landscape image
ps <- circularProjection(ps, k = 2, pdist = 0.4)

# Plot a 2D-landscape image
plotPathwaySpace(ps)