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Annotation Functions for PathwaySpace Plots

Source: R/annotation-pspace.R
annotation_pspace.Rd

annotation_pspace_signal() annotates a ggplot-based PathwaySpace plot with the projected signal layer, rendered as a raster heatmap bounded to the normalized unit space [0, 1].

Usage

annotation_pspace_signal(
  ps,
  title = activeFeature(ps),
  colors = pspace.cols(),
  bg.color = "grey95",
  si.color = "grey85",
  si.alpha = 1,
  zlab = "Density",
  zlim = NULL,
  slices = 25,
  interpolate = FALSE,
  ...
)

Arguments

ps

A PathwaySpace object containing a valid signal projection. Run circularProjection or polarProjection before calling this function.

title

A string used as the plot title. Defaults to the active feature name returned by activeFeature.

colors

A character vector of colors used to build the signal palette. Defaults to pspace.cols.

bg.color

A string specifying the background color, used for zero-signal or masked regions. Defaults to "grey95".

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.

zlab

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

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

An integer specifying the number of discrete color levels used to quantize the signal. For "negpos" scale types, this is rounded up to the nearest even number.

interpolate

A logical value indicating whether to apply linear interpolation with geom_raster.

...

Additional parameters passed to the title annotation; see geom_text.

Value

A list of ggplot2 layer objects that can be added to a ggplot() call with +.

See also

circularProjection

Examples

data("gtoy1", package = "RGraphSpace")
ps <- buildPathwaySpace(gtoy1, nrc = 100)
#> Validating arguments...
#> Validating the 'igraph' object...
#> Normalizing node coordinates to graph space...
#> Creating a 'PathwaySpace' object...
vertexSignal(ps) <- 1
ps <- circularProjection(ps)
#> Validating arguments...
#> Using circular projection...
#> Mapping 'x' and 'y' coordinates...
#> Running signal convolution...

if (FALSE) { # \dontrun{
ggplot(ps) +
  annotation_pspace_signal(ps, si.alpha = 0.8) +
  theme_gspace_coords(is_norm = TRUE)
} # }