renderSbgn: Overlay omics data on a SBGN pathway graph and output image...

In datapplab/SBGNview: "SBGNview: Data Analysis, Integration and Visualization on SBGN Pathways"

Overlay omics data on a SBGN pathway graph and output image files.

Description

This function is not intended to be used directly. Use SBGNview instead. Some input arguments can be better prepared by SBGNview.

Usage

renderSbgn(
  input.sbgn,
  output.file,
  output.formats,
  sbgn.id.attr,
  glyphs.user = list(),
  arcs.user = list(),
  arcs.info = "straight",
  compartment.layer.info = "original",
  user.data = matrix("no.user.data", nrow = 1),
  if.plot.svg = TRUE,
  key.pos = "topright",
  color.panel.scale = 1,
  color.panel.n.grid = 21,
  col.gene.low = "green",
  col.gene.high = "red",
  col.gene.mid = "gray",
  col.cpd.low = "blue",
  col.cpd.high = "yellow",
  col.cpd.mid = "gray",
  min.gene.value = -1,
  max.gene.value = 1,
  mid.gene.value = 0,
  min.cpd.value = -1,
  max.cpd.value = 1,
  mid.cpd.value = 0,
  pathway.name = "",
  pathway.name.font.size = 1,
  if.plot.cardinality = FALSE,
  multimer.margin = 5,
  compartment.opacity = 1,
  auxiliary.opacity = 1,
  if.plot.annotation.nodes = FALSE,
  inhibition.edge.end.shift = 5,
  edge.tip.size = 6,
  if.use.number.for.long.label = FALSE,
  label.spliting.string = c(" ", ":", "-", ";", "/", "_"),
  complex.compartment.label.margin = 8,
  if.write.shorter.label.mapping = TRUE,
  font.size = 3,
  logic.node.font.scale = 3,
  status.node.font.scale = 3,
  node.width.adjust.factor = 2,
  font.size.scale.gene = 3,
  font.size.scale.cpd = 3,
  font.size.scale.complex = 1.1,
  font.size.scale.compartment = 1.6,
  if.scale.complex.font.size = FALSE,
  if.scale.compartment.font.size = FALSE,
  node.width.adjust.factor.compartment = 0.02,
  node.width.adjust.factor.complex = 0.02,
  text.length.factor = 2,
  text.length.factor.macromolecule = 2,
  text.length.factor.compartment = 2,
  text.length.factor.complex = 2,
  space.between.color.panel.and.entity = 100,
  global.parameters.list = NULL
)

Arguments

input.sbgn	A character string. The path to a local SBGN-ML file.
output.file, output.formats, sbgn.id.attr	These parameters are the same as the ones in SBGNview. Please see SBGNview for more details.
glyphs.user	A list, optional. Each element is a 'glyph' object. The element names are glyph IDs (attribute 'id' of XHTML element 'glyph'). Note this is not affected by parameter 'sbgn.id.attr'. The glyph elements contain glyph meta-data for plotting (e.g. text size, border width, border color etc.). Please see the glyph-class documentation for more information. By default, SBGNview will run without this argument and return a glyph list extracted from the SBGN file. User can then customize this glyph list and assign it to 'glyphs.user' in the next SBGNview run to update the graph.
arcs.user	A list, optional. Each member is an 'arc' object. The element names are arc IDs (the value of 'id' attribute in XHTML element 'arc' or 'arc.spline' in the SBGN-ML file). Some SBGN-ML files have no arc IDs, in this case SBGNview will create an arc ID using 'source' and 'target' node IDs). The arc object contains arc meta-data for plotting (e.g. arc line width, line color etc.). Please see the arc-class documentation for more information. By default, SBGNview() will run without this argument and return an arc list. User can then customize this arc list and assign it to 'arcs.user' in the next SBGNview() run to update the arcs.
arcs.info	A character string. It should be one of the following: 'parse splines', 'straight' or a string of svg code of arcs. If it is 'parse splines', this function will look for XML element 'arc.spline' in the SBGN-ML file and plot spline arcs. If it is 'straight', the function will look for element 'arc' and plot straight line arcs. If it is a string of svg code, it will write this code directly to the output svg file.
compartment.layer.info	A character vector. It is a vector containing the IDs of all compartment glyphs. It determins the layer arrangement of compartments. Compartments will be drawn following their sequence in this vector. Therefore, a compartment that appears later in the vector will be on the front layer and covers the compartments that are before it in this vector. This is important. In some cases compartments have overlap. This layer information ensures that a glyph laying in the overlapped region belongs to the compartment on the top layer.
user.data	A list. It holds both gene/protein data and compound data. Names are gene or compounds, each element is a numeric vector of the omics data of each molecule.
if.plot.svg	Logical. Default: T. Whether to generate svg code or only parse SBGN-ML file. This parameter is for internal use only.
key.pos	A character string. The position of color panel. Default: 'topright'. Accepts one of 'bottomleft' , 'bottomright', 'topright', or 'topleft'. The ideal position for the color panel is 'topright' or 'bottomright'. If 'topleft' or 'bottomleft' are passed in, the key.pos location will default to 'topright'. If key.pos is set to 'none', the pathway name and color panel won't be plotted.
color.panel.scale	Numeric. Default: 1. It controls the relative size of color scheme panel.
color.panel.n.grid	Numeric. Default: 21. How many colors does the color scheme show.
col.gene.low	A character string. Default: 'green'. Color panel's color representing low gene data values.
col.gene.high	A character string. Default: 'red'. Color panel's color representing high gene data values.
col.gene.mid	A character string. Default: 'gray'. Color panel's color representing mid range gene data values.
col.cpd.low	A character string. Default: 'blue'. Color panel's color representing low compound data values.
col.cpd.high	A character string. Default: 'yellow'. Color panel's color representing high compound data values.
col.cpd.mid	A character string. Default: 'gray'. Color panel's color representing mid range compound data values.
min.gene.value	Numeric. Default: -1. Color panel's min value for gene data. Values smaller than this will have the same color as min value.
max.gene.value	Numeric. Default: 1. Color panel's max value for gene data. Values greater than this will have the same color as the max value.
mid.gene.value	Numeric. Default: 0. Color panel's mid value for gene data.
min.cpd.value	Numeric. Default: -1. Color panel's min value for compound data. Values smaller than this will have the same color as min value.
max.cpd.value	Numeric. Default: 1. Color panel's max value for compound data. Values greater than this will have the same color as max value.
mid.cpd.value	Numeric. Default: 0. Color panel's mid value for compound data.
pathway.name	List containing two elements: 1. pathway name 2. stamp information. See argument description in SBGNview function to change/update pathway name displayed on graph.
pathway.name.font.size	Numeric. Default: 1. When pathway names are plotted on graph, this parameter controls their font size.
if.plot.cardinality	Logical. Default: F. If plot cardinality glyphs.
multimer.margin	Numeric. Default: 5. For multimers, they are represented by two partly overlapped shapes (rectangle, ellipse etc.). This parameter controls how much the two shapes overlap.
compartment.opacity	Numeric. Default: 1. Controls how transparent the compartments are.
auxiliary.opacity	Numeric. Default: 1. Controls opacity of auxiliary glyphs.
if.plot.annotation.nodes	Logical. Default: F. Some SBGN-ML files have 'annotation' glyphs. By default we don't plot them.
inhibition.edge.end.shift	Numeric. Default: 5. The tip of 'inhibition' arcs is a line segment. Sometimes it overlaps with target glyph's border. We can shift it along the arc to prevent the overlap.
edge.tip.size	Numeric. Default: 6. Control size of edge tips.
if.use.number.for.long.label	Logical. Default: F. If the label is too long, we can create a shorter name for it. e.g. 'macromolecule_1'.
label.spliting.string	A character vector. Default: c(' ','-',';','/','_'). When we split text into multiple lines, these characters will be used to split label (where a new line can be created).
complex.compartment.label.margin	Numeric. Default: 8. Move the label text vertically for compartment and complex.
if.write.shorter.label.mapping	Logical. Default: T. If if.use.number.for.long.label is 'T', we can write the mapping between shorter name and the original label to a text file.
font.size	Numeric. Default: 3. Affects font size of all types of glyphs.
logic.node.font.scale	Numeric. Default: 3. Controls the size of logical glyphs ('and', 'or', 'not' etc.).
status.node.font.scale	Numeric. Default: 3. Scale the font size for status variable and unit of information nodes.
node.width.adjust.factor	Numeric. Default: 2. Change font size according to the width of its glyph. If the glyph is too large (e.g. compartment), its label may look too small. Then we can enlarge the label in proportion to the width of the glyph. It affects all types of glyphs.
font.size.scale.gene	Numeric. Default: 3. Scales font size according to the node's width for large compartments. Only affect font size of 'macromolecule' glyphs.
font.size.scale.cpd	Numeric. Default: 3. Scales font size according to the node's width for large compartments. Only affects font size of 'simple chemical' glyphs.
font.size.scale.complex	Numeric. Default: 1.1. Scale the font size of a complex.
font.size.scale.compartment	Numeric. Default: 1.6. Scale the font size of a compartment.
if.scale.complex.font.size	Logical. Default: F. Whether to scale complex font size according to its width. If set to 'T', the 'node.width.adjust.factor.complex' argument can be used to specify the scale factor.
if.scale.compartment.font.size	Logical. Default: F. Whether to scale compartment font size according to its width. If set to 'T', the 'node.width.adjust.factor.compartment' argument can be used to specify the scale factor.
node.width.adjust.factor.compartment	Numeric. Default: 0.02. How much the font size should change in proportion to the width of compartment. The font is scaled only if 'if.scale.compartment.font.size' is set to 'T'. To find the best scale factor which works you, start with 0.02 (default) and incrementally increase that value.
node.width.adjust.factor.complex	Numeric. Default: 0.02. How much the font size should change in proportion to the width of complex. The font is scaled only if 'if.scale.complex.font.size' is set to 'T'. To find the best scale factor which works you, start with 0.02 (default) and incrementally increase that value.
text.length.factor	Numeric. Default: 2. How wide the wrapped text should be. If text is longer than the width controled by this parameter, the text is split into a new line, but only at characters in 'label.spliting.string'. Controls all glyphs.
text.length.factor.macromolecule	Numeric. Default: 2. Used to determine label text wrapping based on number of characters, font size, and node width for macromolecule glyphs.
text.length.factor.compartment	Numeric. Default: 2. Used to determine label text wrapping based on number of characters, font size, and node width for compartment glyphs.
text.length.factor.complex	Numeric. Default: 2. Used to determine label text wrapping based on number of characters, font size, and node width for complex glyphs.
space.between.color.panel.and.entity	Numeric. Default: 100. The minimum space between color panel and any other object in the graph. The function will always try to find a location of the color panel to minimize empty space on the whole graph. This parameter controls how close it can reach a glyph.
global.parameters.list	List. A record of parameters fed to 'renderSbgn' for reuse. It will over-write other parameters. It is not designed to be used directly.

Value

A list of three elements: glyphs.list, arcs.list, global.parameters.list

Examples

## Not run: 
data(pathways.info)
SBGNview.obj <- SBGNview(simulate.data = TRUE,
                         sbgn.dir = './',
                         input.sbgn = 'P00001',
                         output.file = './test.local.file',
                         output.formats = c('pdf'),
                         min.gene.value = -1,
                         max.gene.value = 1)
 
## End(Not run)

datapplab/SBGNview documentation built on June 20, 2022, 9:55 p.m.