| Title: | Spatial Projection of Network Signals along Geodesic Paths |
|---|---|
| Description: | For a given graph containing vertices, edges, and a signal associated with the vertices, the 'PathwaySpace' package performs a convolution operation, which involves a weighted combination of neighboring vertices and their associated signals. The package then uses a decay function to project these signals, creating geodesic paths on a 2D-image space. 'PathwaySpace' could have various applications, such as visualizing and analyzing network data in a graphical format that highlights the relationships and signal strengths between vertices. It can be particularly useful for understanding the influence of signals through complex networks. By combining graph theory, signal processing, and visualization, the 'PathwaySpace' package provides a novel way of representing and analyzing graph data. |
| Authors: | Victor Apolonio [ctr],
Vinicius Chagas [ctr],
Mauro Castro [aut, cre] |
| Maintainer: | Mauro Castro <[email protected]> |
| License: | Artistic-2.0 |
| Version: | 1.0.0 |
| Built: | 2024-11-12 02:29:32 UTC |
| Source: | https://github.com/sysbiolab/pathwayspace |
buildPathwaySpace is a constructor of
PathwaySpace-class objects.
buildPathwaySpace(g, nrc = 500, mar = 0.075, verbose = TRUE)buildPathwaySpace(g, nrc = 500, mar = 0.075, verbose = TRUE)
g |
An |
nrc |
A single positive integer indicating the number of rows and columns (in pixels) for a square image matrix. This argument will affect the resulting image size and resolution. |
mar |
A single numeric value (in |
verbose |
A single logical value specifying to display detailed
messages (when |
A preprocessed PathwaySpace class object.
Vinicius Chagas, Victor Apolonio, Mauro Castro, and TCGA Network.
# 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# 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
A data frame listing 'GeneSymbol' and 'Entrez' IDs from the COSMIC-CGC database (Sondka et al., 2020). These genes are used to demonstrate the PathwaySpace's summit mapping pipeline, which assigns summits to an image space.
data(CGC_20211118)data(CGC_20211118)
data.frame
A data.frame object.
COSMIC-CGC database (release v95, tier 1 collection).
Sondka et al. The COSMIC Cancer Gene Census: describing genetic dysfunction across all human cancers. Nat Rev Cancer 18, 696-705, 2018. Doi: 10.1038/s41568-018-0060-1.
data(CGC_20211118)data(CGC_20211118)
circularProjection implements a convolution
algorithm to project signal across a 2D-coordinate system.
## S4 method for signature 'PathwaySpace' circularProjection( pts, knn = 8, pdist = 0.15, rescale = TRUE, verbose = TRUE, decay_fun = weibullDecay, ... )## S4 method for signature 'PathwaySpace' circularProjection( pts, knn = 8, pdist = 0.15, rescale = TRUE, verbose = TRUE, decay_fun = weibullDecay, ... )
pts |
A PathwaySpace class object. |
knn |
A single positive integer determining the k-nearest signal sources used in the signal convolution operation. |
pdist |
A term (in |
rescale |
A single logical value indicating whether to rescale
the signal. If the signal |
verbose |
A single logical value specifying to display detailed
messages (when |
decay_fun |
A signal decay function. Available: 'Weibull',
'exponential', and 'linear' functions (see |
... |
Additional arguments passed to the decay function. |
A preprocessed PathwaySpace class object.
Vinicius Chagas, Victor Apolonio, Mauro Castro, and TCGA Network.
# 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)# 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)
The expDecay function is used by PathwaySpace's methods
for signal convolution and projection.
expDecay(x, signal, decay = 0.999, ...)expDecay(x, signal, decay = 0.999, ...)
x |
A numeric vector of distances (in [0,1]). |
signal |
A single numeric value representing a signal. |
decay |
The rate (in [0,1]) at which the signal decays.
This term indicates how much the |
... |
Not used; argument implemented for call compatibility with
the |
A numeric vector.
Vinicius Chagas, Victor Apolonio, and Mauro Castro ([email protected])
x <- c(1:100) / 100 y <- expDecay(x, 1) plot(x, y)x <- c(1:100) / 100 y <- expDecay(x, 1) plot(x, y)
getPathwaySpace retrives information from
individual slots available in a PathwaySpace object.
## S4 method for signature 'PathwaySpace' getPathwaySpace(pts, what = "status")## S4 method for signature 'PathwaySpace' getPathwaySpace(pts, what = "status")
pts |
A preprocessed PathwaySpace class object |
what |
A single character value specifying which information should be retrieved from the slots. Options: 'graph','gxy','gxyz','pars','misc','status','summits', 'summit_mask', and 'summit_contour'. |
Content from slots in the PathwaySpace object.
# 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 # Get the 'status' slot in pts status <- getPathwaySpace(pts, what = 'status')# 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 # Get the 'status' slot in pts status <- getPathwaySpace(pts, what = 'status')
An image matrix used for workflow demonstrations.
data(gimage)data(gimage)
matrix
An image matrix.
This package.
data(gimage)data(gimage)
Small 'igraph' objects used for workflow demonstrations. All graphs include 'x', 'y', and 'name' vertex attributes.
data(gtoy1)data(gtoy1)
igraph
A pre-processed igraph object.
This package.
data(gtoy1) data(gtoy2)data(gtoy1) data(gtoy2)
A list with Human gene symbols from the MSigDB's Hallmark gene set collection (Liberzon et al., 2015). These gene sets are used to demonstrate the PathwaySpace's summit mapping pipeline, which assigns summits to an image space.
data(Hallmarks_v2023_1_Hs_symbols)data(Hallmarks_v2023_1_Hs_symbols)
list
A list object.
MSigDB database (v2023.1).
Liberzon et al. The Molecular Signatures Database (MSigDB) hallmark gene set collection. Cell Systems 1(5):417-425, 2015 Doi: 10.1016/j.cels.2015.12.004
data(Hallmarks_v2023_1_Hs_symbols)data(Hallmarks_v2023_1_Hs_symbols)
Get length of a PathwaySpace object.
## S4 method for signature 'PathwaySpace' length(x)## S4 method for signature 'PathwaySpace' length(x)
x |
A PathwaySpace class object. |
A non-negative integer of length 1.
data('gtoy1', package = 'PathwaySpace') pts <- buildPathwaySpace(gtoy1, nrc = 100) length(pts)data('gtoy1', package = 'PathwaySpace') pts <- buildPathwaySpace(gtoy1, nrc = 100) length(pts)
The linearDecay function is used by PathwaySpace's
methods for signal convolution and projection.
linearDecay(x, signal, ...)linearDecay(x, signal, ...)
x |
A numeric vector of distances (in [0,1]). |
signal |
A single numeric value representing a signal. |
... |
Not used; argument implemented for call compatibility with
|
A numeric vector.
Vinicius Chagas, Victor Apolonio, and Mauro Castro ([email protected])
x <- c(1:100) / 100 y <- linearDecay(x, 1) plot(x, y)x <- c(1:100) / 100 y <- linearDecay(x, 1) plot(x, y)
Get and set 'vertex' names of a PathwaySpace class object.
## S4 method for signature 'PathwaySpace' names(x)## S4 method for signature 'PathwaySpace' names(x)
x |
A PathwaySpace class object. |
A character vector.
data('gtoy1', package = 'PathwaySpace') pts <- buildPathwaySpace(gtoy1, nrc = 100) names(pts)data('gtoy1', package = 'PathwaySpace') pts <- buildPathwaySpace(gtoy1, nrc = 100) names(pts)
Calculate a pathway space distance between two vectors.
pathDistances(gdist, from, to, nperm = 1000, verbose = TRUE)pathDistances(gdist, from, to, nperm = 1000, verbose = TRUE)
gdist |
A distance matrix computed by the igraph's |
from |
A vector with valid vertex names. |
to |
A vector with valid vertex names. |
nperm |
Number of permutations. |
verbose |
A single logical value specifying to display detailed
messages (when |
A list with pathway space distances and a 'ggplot' object.
# Load a vertex-wise distance matrix (distance between nodes in a graph) data("gdist.toy", package = "PathwaySpace") # Get two vertex lists from <- sample(colnames(gdist.toy), 50) to <- sample(colnames(gdist.toy), 50) # Calculate distances between lists, and between random lists res <- pathDistances(gdist.toy, from, to) names(res) # "p_dist" "z_score"# Load a vertex-wise distance matrix (distance between nodes in a graph) data("gdist.toy", package = "PathwaySpace") # Get two vertex lists from <- sample(colnames(gdist.toy), 50) to <- sample(colnames(gdist.toy), 50) # Calculate distances between lists, and between random lists res <- pathDistances(gdist.toy, from, to) names(res) # "p_dist" "z_score"
PathwaySpace: An S4 class for signal propagation on image spaces.
An S4 class object.
vertexA character vector with vertex names.
vsignalA numerical vector with vertex signals.
vweightA numerical vector with vertex weights.
edgesA data frame with edges.
gxyA data frame with xy-vertex coordinates (numerical).
gxyzA numerical matrix with x-cols and y-rows coordinates, and a z-signal.
parsA list with parameters.
miscA list with intermediate objects for downstream methods.
statusA vector containing the processing status of the PathwaySpace object.
see buildPathwaySpace constructor.
Mauro Castro, [email protected]
This igraph object was created from a 'sif' file available from the Pathway Commons V12 (Rodchenkov et al., 2020), which was filtered to keep interactions from the following sources: CTD, Recon, HumanCyc, DrugBank, MSigDB, DIP, BioGRID, IntAct, BIND, and PhosphoSite. The igraph was additionally pruned and laid out by a force-directed algorithm aiming signal projection on PathwaySpace's images. Edges with the smallest betweenness centrality were pruned using 'backward elimination' and 'forward selection' strategies. The resulting graph represents the main connected component with the minimum number of edges.
data(PCv12_pruned_igraph)data(PCv12_pruned_igraph)
igraph
An igraph object.
Chris Wong, Mauro Castro, and TCGA Network.
Pathway Commons V12.
Rodchenkov et al. Pathway Commons 2019 Update: integration, analysis and exploration of pathway data. Nucleic Acids Research 48(D1):D489–D497, 2020. doi:10.1093/nar/gkz946
data(PCv12_pruned_igraph) ## Suggestion to vizualize this igraph in R: library(RGraphSpace) plotGraphSpace(PCv12_pruned_igraph)data(PCv12_pruned_igraph) ## Suggestion to vizualize this igraph in R: library(RGraphSpace) plotGraphSpace(PCv12_pruned_igraph)
Accessory function to plot pathway space distances.
plotPathDistances(pdist, z.transform = FALSE)plotPathDistances(pdist, z.transform = FALSE)
pdist |
A list generated by the |
z.transform |
A single logical value specifying to convert pathway distances into z-score values. |
A 'ggplot' object.
# Load a vertex-wise distance matrix (distance between nodes in a graph) data("gdist.toy", package = "PathwaySpace") # Get two gene lists from <- sample(colnames(gdist.toy), 50) to <- sample(colnames(gdist.toy), 50) # Calculate distances between lists, and between random lists res <- pathDistances(gdist.toy, from, to) # Plot observed and null distances plotPathDistances(res)# Load a vertex-wise distance matrix (distance between nodes in a graph) data("gdist.toy", package = "PathwaySpace") # Get two gene lists from <- sample(colnames(gdist.toy), 50) to <- sample(colnames(gdist.toy), 50) # Calculate distances between lists, and between random lists res <- pathDistances(gdist.toy, from, to) # Plot observed and null distances plotPathDistances(res)
plotPathwaySpace is a wrapper function to
create dedicated ggplot graphics for PathwaySpace-class objects.
## S4 method for signature '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 )## S4 method for signature '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 )
pts |
A PathwaySpace class object. |
colors |
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. |
trim.colors |
An vector with 5 positive integer numbers. This argument can be used to adjust the proportion of each color tone in the palette. |
bg.color |
A single color for background. |
theme.name |
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. |
title |
A string for the title. |
font.size |
A single numeric value passed to ggplot themes. |
font.color |
A single color passed to ggplot themes. |
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. |
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 |
grid.color |
A color passed to |
add.contour |
A logical value indicating whether to add contour
lines to 'summits' (see |
contour.color |
A color passed to |
label.summits |
A logical value indicating whether to label summits, (when summits are available). |
marks |
A logical value indicating whether to add 'marks' to vertex positions. Alternatively, this could be a vector listing vertex names. |
mark.size |
A font size argument passed to
|
mark.color |
A color passed to |
mark.padding |
A box padding argument passed to
|
mark.line.width |
A line width argument passed to
|
use.dotmark |
A logical value indicating whether "marks" should be represented as dots. |
A ggplot-class object.
Vinicius Chagas, Victor Apolonio, Mauro Castro, and TCGA Network.
# 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)# 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)
polarProjection implements a convolution algorithm
to project a signal across a 2D-coordinate system.
## S4 method for signature 'PathwaySpace' polarProjection( pts, knn = 8, pdist = 0.5, rescale = TRUE, theta = 180, directional = FALSE, verbose = TRUE, decay_fun = weibullDecay, ... )## S4 method for signature 'PathwaySpace' polarProjection( pts, knn = 8, pdist = 0.5, rescale = TRUE, theta = 180, directional = FALSE, verbose = TRUE, decay_fun = weibullDecay, ... )
pts |
A PathwaySpace class object. |
knn |
A single positive integer determining the k-nearest signal sources used in the signal convolution operation. |
pdist |
A term (in |
rescale |
A single logical value indicating whether to rescale
the signal. If the signal |
theta |
Angle of projection (degrees in |
directional |
If directional edges are available, this argument can be used to orientate the signal projection on directed graphs. |
verbose |
A single logical value specifying to display detailed
messages (when |
decay_fun |
A signal decay function. Available: 'Weibull',
'exponential', and 'linear' functions (see |
... |
Additional arguments passed to the decay function. |
A preprocessed PathwaySpace class object.
Vinicius Chagas, Victor Apolonio, Mauro Castro, and TCGA Network.
# 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 <- polarProjection(pts)# 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 <- polarProjection(pts)
A simple vector of colors for PathwaySpace images.
pspace.cols(n = 5)pspace.cols(n = 5)
n |
Number of colors. |
A vector with hexadecimal color codes.
pspace.cols()pspace.cols()
silhouetteMapping constructs an image baseline used
to outline the graph layout in a PathwaySpace image.
## S4 method for signature 'PathwaySpace' silhouetteMapping(pts, baseline = 0.01, pdist = 0.05, verbose = TRUE)## S4 method for signature 'PathwaySpace' silhouetteMapping(pts, baseline = 0.01, pdist = 0.05, verbose = TRUE)
pts |
A PathwaySpace class object. |
baseline |
A fraction (in |
pdist |
A term (in |
verbose |
A single logical value specifying to display detailed
messages (when |
A preprocessed PathwaySpace class object.
Vinicius Chagas, Victor Apolonio, Mauro Castro, and TCGA Network.
# 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)# 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)
The summitMapping method implements a segmentation
strategy to identify summits on a 2D-landscape image
(see summitWatershed).
## S4 method for signature 'PathwaySpace' summitMapping( pts, maxset = 30, minsize = 30, threshold = 0.5, verbose = TRUE, segm_fun = summitWatershed, ... )## S4 method for signature 'PathwaySpace' summitMapping( pts, maxset = 30, minsize = 30, threshold = 0.5, verbose = TRUE, segm_fun = summitWatershed, ... )
pts |
A PathwaySpace class object. |
maxset |
A single positive integer indicating the maximum number of summits to be returned by the segmentation function. |
minsize |
A single positive integer indicating the minimum size of the summits. |
threshold |
A threshold provided as a fraction (in |
verbose |
A single logical value specifying to display detailed
messages (when |
segm_fun |
A segmentation function used to detect summits
(see |
... |
Additional arguments passed to the segmentation function. |
A preprocessed PathwaySpace class object.
Vinicius Chagas, Victor Apolonio, Mauro Castro, and TCGA Network.
# 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 summits in a 2D-landscape image pts <- summitMapping(pts)# 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 summits in a 2D-landscape image pts <- summitMapping(pts)
The summitWatershed function implements a segmentation
strategy to identify summits within a landscape image generated by the
PathwaySpace package. This function is entirely coded in R, which helps
alleviating users from the task of loading an excessive number of
dependencies. Nonetheless, while this novel implementation prevents
the burden a 'dependency heaviness', it still requires optimization
as it currently exhibits slower performance compared to well-established
implementations such as the watershed function from the EBImage package.
The summitWatershed maintain a certain level of compatibility
with the EBImage's watershed function, and both can be used in the
PathwaySpace package.
summitWatershed(x, tolerance = 0.1, ext = 1)summitWatershed(x, tolerance = 0.1, ext = 1)
x |
A 2D-numeric array in which each point represents the coordinates of a signal in a landscape image. |
tolerance |
The minimum signal intensity of a summit (in [0,1]), representing a fraction of the maximum signal intensity. |
ext |
Radius (in pixels) for detecting neighboring objects. |
A matrix with labeled summits.
Vinicius Chagas, Victor Apolonio, and Mauro Castro ([email protected])
# Load a demo landscape image data('gimage', package = 'PathwaySpace') # Scale down the image for a quicker demonstration gimage <- gimage[200:300, 200:300] # Check signal range range(gimage, na.rm = TRUE) # [1] 0 1 # Check image image(gimage) # Threshold the signal intensity, for example: gimage[gimage < 0.5] <- 0 # Run summit segmentation gmask <- summitWatershed(x = gimage) # Check resulting image mask image(gimage)# Load a demo landscape image data('gimage', package = 'PathwaySpace') # Scale down the image for a quicker demonstration gimage <- gimage[200:300, 200:300] # Check signal range range(gimage, na.rm = TRUE) # [1] 0 1 # Check image image(gimage) # Threshold the signal intensity, for example: gimage[gimage < 0.5] <- 0 # Run summit segmentation gmask <- summitWatershed(x = gimage) # Check resulting image mask image(gimage)
Get or set 'signal' for a PathwaySpace class object.
## S4 method for signature 'PathwaySpace' vertexSignal(pts) ## S4 replacement method for signature 'PathwaySpace' vertexSignal(pts) <- value## S4 method for signature 'PathwaySpace' vertexSignal(pts) ## S4 replacement method for signature 'PathwaySpace' vertexSignal(pts) <- value
pts |
A PathwaySpace class object. |
value |
A numeric vector with values representing signal intensities. This vector should be aligned to the "vertex" slot. |
A numeric vector.
data('gtoy1', package = 'PathwaySpace') pts <- buildPathwaySpace(gtoy1, nrc = 100) vertexSignal(pts)data('gtoy1', package = 'PathwaySpace') pts <- buildPathwaySpace(gtoy1, nrc = 100) vertexSignal(pts)
Get or set 'weights' for a PathwaySpace class object.
## S4 method for signature 'PathwaySpace' vertexWeight(pts) ## S4 replacement method for signature 'PathwaySpace' vertexWeight(pts) <- value## S4 method for signature 'PathwaySpace' vertexWeight(pts) ## S4 replacement method for signature 'PathwaySpace' vertexWeight(pts) <- value
pts |
A PathwaySpace class object. |
value |
A numeric vector with values representing vertex weights. This vector should be aligned to the "vertex" slot. |
A numeric vector.
data('gtoy1', package = 'PathwaySpace') pts <- buildPathwaySpace(gtoy1, nrc = 100) vertexWeight(pts)data('gtoy1', package = 'PathwaySpace') pts <- buildPathwaySpace(gtoy1, nrc = 100) vertexWeight(pts)
The weibullDecay function is used by
PathwaySpace's methods for signal convolution and projection.
weibullDecay(x, signal, decay = 0.999, shape = 1.05)weibullDecay(x, signal, decay = 0.999, shape = 1.05)
x |
A numeric vector of distances (in [0,1]). |
signal |
A single numeric value representing a signal. |
decay |
The rate (in [0,1]) at which the signal decays.
This term indicates how much the |
shape |
A parameter (>=1) of a Weibull function. When |
A numeric vector.
Vinicius Chagas, Victor Apolonio, and Mauro Castro ([email protected])
x <- c(1:100) / 100 y <- weibullDecay(x, 1) plot(x, y)x <- c(1:100) / 100 y <- weibullDecay(x, 1) plot(x, y)