plotPathwaySpace is a wrapper function to
create dedicated ggplot graphics for PathwaySpace-class objects.
# S4 method for PathwaySpace
plotPathwaySpace(
pts,
colors = pspace.cols(),
trim.colors = c(3, 2, 1, 2, 3),
bg.color = "grey85",
theme.name = c("th0", "th1", "th2", "th3"),
title = "PathwaySpace",
font.size = 1,
font.color = "white",
xlab = "Pathway coordinates 1",
ylab = "Pathway coordinates 2",
zlab = "Density",
zlim = NULL,
slices = 25,
add.grid = TRUE,
grid.color = "white",
add.contour = TRUE,
contour.color = "white",
label.summits = TRUE,
marks = FALSE,
mark.size = 3,
mark.color = "white",
mark.padding = 0.5,
mark.line.width = 0.5,
use.dotmark = FALSE
)A ggplot-class object.
A PathwaySpace class object.
A vector of colors. Each color is a specific tone used to create a customized color palette that matches the signal type projected in the image space, such as binary or numeric values in (-Inf, +Inf). The palette will be created with 5-color tones, interpolated according to the provided sequence in the vector of colors. The proportion of each color tone can be adjusted by the 'trim.colors' argument. The primary objective of this color palette construction is to enhance the visibility of summits and valleys in the image space. If you wish to bypass the automatic palette generation and use the 'colors' input as-is, simply set 'trim.colors' to NULL.
An vector with 5 positive integer numbers. This argument can be used to adjust the proportion of each color tone in the palette.
A single color for background.
Name of a custom PathwaySpace theme. These themes (from 'th0' to 'th3') consist mainly of preconfigured ggplot settings, which the user can subsequently fine-tune within the resulting ggplot object.
A string for the title.
A single numeric value passed to ggplot themes.
A single color passed to ggplot themes.
The title for the 'x' axis of a 2D-image space.
The title for the 'y' axis of a 2D-image space.
The title for the 'z' axis of the image signal.
The 'z' limits of the plot (a numeric vector with two numbers). If NULL, limits are determined from the range of the input values.
A single positive integer value used to split the image signal into equally-spaced intervals.
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).
A color passed to geom_point.
A logical value indicating whether to add contour
lines to 'summits' (see summitMapping).
A color passed to geom_tile.
A logical value indicating whether to label summits, (when summits are available).
A logical value indicating whether to add 'marks' to vertex positions. Alternatively, this could be a vector listing vertex names.
A font size argument passed to
geom_text.
A color passed to geom_text_repel.
A box padding argument passed to
geom_text_repel.
A line width argument passed to
geom_text_repel.
A logical value indicating whether "marks" should be represented as dots.
Vinicius Chagas, Victor Apolonio, Mauro Castro, and TCGA Network.
circularProjection
# Load a demo igraph
data('gtoy1', package = 'PathwaySpace')
# Create a new PathwaySpace object
pts <- buildPathwaySpace(gtoy1, nrc = 100)
# note: adjust 'nrc' to increase image resolution
# Create a 2D-landscape image
pts <- circularProjection(pts)
# Map graph silhouette
pts <- silhouetteMapping(pts)
# Plot a 2D-landscape image
plotPathwaySpace(pts)
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