node.color: Code molecular data as pseudo colors on the pathway graph

In datapplab/pathview: a tool set for pathway based data integration and visualization

Code molecular data as pseudo colors on the pathway graph

Description

node.color converts the mapped molecular (gene, protein or metabolite etc) data as pseudo colors on pathway nodes. col.key draws color key(s) for mapped molecular data on the pathway graph.

Usage

node.color(plot.data = NULL, discrete=FALSE, limit, bins, both.dirs =
TRUE, low = "green", mid = "gray", high = "red", na.col = "transparent",
trans.fun = NULL)
col.key(discrete=FALSE, limit = 1, bins = 10, cols = NULL, both.dirs =
TRUE, low = "green", mid = "gray", high = "red", graph.size, node.size,
size.by.graph = TRUE, key.pos = "topright", off.sets = c(x = 0, y = 0),
align = "n", cex = 1, lwd = 1)

Arguments

plot.data	the result returned by node.map function. It is a data.frame composed of parsed KGML data and summary molecular data for each mapped node. Rows are mapped nodes, and columns are parsed or mapped node data. Check node.map for details.
discrete	logical, whether to treat the molecular data or node summary data as discrete. d discrete=FALSE, otherwise, mol.data will be a charactor vector of molecular IDs.
limit	a list of two numeric elements with "gene" and "cpd" as the names. This argument specifies the limit values for gene.data and cpd.data when converting them to pseudo colors. Each element of the list could be of length 1 or 2. Length 1 suggests discrete data or 1 directional (positive-valued) data, or the absolute limit for 2 directional data. Length 2 suggests 2 directional data. Default limit=list(gene=0.5, cpd=1).
bins	a list of two integer elements with "gene" and "cpd" as the names. This argument specifies the number of levels or bins for gene.data and cpd.data when converting them to pseudo colors. Default limit=list(gene=10, cpd=10).
both.dirs	a list of two logical elements with "gene" and "cpd" as the names. This argument specifies whether gene.data and cpd.data are 1 directional or 2 directional data when converting them to pseudo colors. Default limit=list(gene=TRUE, cpd=TRUE).
trans.fun	a list of two function (not character) elements with "gene" and "cpd" as the names. This argument specifies whether and how gene.data and cpd.data are transformed. Examples are log, abs or users' own functions. Default limit=list( gene=NULL, cpd=NULL).
low, mid, high	each is a list of two colors with "gene" and "cpd" as the names. This argument specifies the color spectra to code gene.data and cpd.data. When data are 1 directional (TRUE value in both.dirs), only mid and high are used to specify the color spectra. Default spectra (low-mid-high) "green"-"gray"-"red" and "blue"-"gray"-"yellow" are used for gene.data and cpd.data respectively. The values for 'low, mid, high' can be given as color names ('red'), plot color index (2=red), and HTML-style RGB, ("\#FF0000"=red).
na.col	color used for NA's or missing values in gene.data and cpd.data. d na.col="transparent".
cols	character, specifying a discrete spectrum of colors to be plotted as color key. Note this argument is usually NULL (default), otherwise, the number of discrete colors has to match bins.
graph.size	numeric vector of length 2, i.e. the sizes (width, height) of the pathway graph panel. This is needed to determine the sizes and exact location of the color key.
node.size	numeric vector of length 2, i.e. the sizes (width, height) of the standard gene nodes (rectangles). This is needed to determine the sizes and exact location of the color key when size.by.graph=FALSE.
size.by.graph	logical, whether to determine the sizes and exact location of the color key with respect to the size of the whole graph panel or that of a single node. Default size.by.graph=TRUE.
key.pos	character, controlling the position of color key(s). Potentail values are "bottomleft", "bottomright", "topleft" and "topright". d key.pos="topright".
off.sets	numeric vector of length 2, with "x" and "y" as the names. This argument specifies the offset values in x and y axes when plotting a new color key, as to avoid overlap with existing color keys or boundaries. Note that the off.sets value is reset and returned each time col.key function is called, as for the reference of plotting the next color key. Default off.sets=c(0,0).
align	character, controlling how the color keys are aligned when needed. Potential values are "x", aligned by x coordinates, and "y", aligned by y coordinates. Default align="x".
cex	A numerical value giving the amount by which legend text and symbols should be scaled relative to the default 1.
lwd	numeric, the line width, a _positive_ number, defaulting to '1'.

Details

node.color converts the mapped molecular data (gene.data or cpd.data) by node.map function into pseudo colors, which then can be plotted on the pathway graph. col.key is used in combination with node.color in pathview, although this function can be used independently for similar tasks.

Value

node.color returns a vector or matrix of colors. Its dimensionality is the same as the corresponding gene.data or cpd.data. col.key plots a color key on existing pathway graph, then returns a updated version of off.sets for the reference of next color key.

Author(s)

Weijun Luo <[e-mail]>

References

Luo, W. and Brouwer, C., Pathview: an R/Bioconductor package for pathway based data integration and visualization. Bioinformatics, 2013, 29(14): 1830-1831, doi: 10.1093/bioinformatics/btt285

See Also

keggview.native and keggview.graph the viwer functions, node.map the node data mapper function.

Examples

xml.file=system.file("extdata", "hsa04110.xml", package = "pathview")
node.data=node.info(xml.file)
names(node.data)
data(gse16873.d)
plot.data.gene=node.map(mol.data=gse16873.d[,1], node.data,
  node.types="gene")
head(plot.data.gene)
cols.ts.gene=node.color(plot.data.gene, limit=1, bins=10)
head(cols.ts.gene)

datapplab/pathview documentation built on March 30, 2024, 9:06 a.m.