Mutation Visualization

Description Usage Arguments Value Author(s)

Visualize protein structure information while optionally plotting location and frequency of events along the length of the protein.

metaCountStructPlot(events, catname = "PRIMARY_TISSUE", requiredCats =
NULL, position =
c("protpos", "protposend"), pfam, pfamLabels = "featureName",  structPred, hydro,
transMem, sigP, xlim, tmposcol = c("start", "end"), main = NULL,
 logscale = TRUE, logbase = 1.506,
scale.factor = 10, colpalette = rev(brewer.pal(11, "RdYlBu")),
legend.step = 0.01, sampleID, subtitle, draw = TRUE, vertGuides = 10,
sequence.counts = NULL)

proteinStructPlot(pfam, structPred, xlim, tmposcol = c("start", "end"),
main = NULL, pfamLabels = "featureName", draw = TRUE, vertGuides = 10)

createProteinImages(events,catname = "PRIMARY_TISSUE",
requiredCats = NULL, position = c("protpos", "protposend"),  pfam,
pfamLabels = "featureName",structPred, hydro, transMem, sigP, xlim,
tmposcol = c("start", "end"), main = NULL, logscale = TRUE,
logbase = 1.506, scale.factor = 10, colpalette =rev(brewer.pal(11,"RdYlBu")),
legend.step = .01, sampleID, subtitle = "Amino Acid Position",
vertGuides = 10, sequence.counts = NULL, metaFileName =
"VariantPlot.svg", structFileName = "StructurePlot.svg", metaHeight,
structHeight, width)

`events`	Data.frame containing the data for the events to count (must include both position (start and end) and category information)
`catname`	Name of the column in events which specifies category.
`requiredCats`	Character vector specifying the categories that must be displayed in the graphic (even in the that they contain no observations). They should be specified in the order they are to appear starting from the bottom of the metaCount section of the plot.. If there are categories observed in the data not found in requiredCats, they are added to the end of the list in the order they appear. If `NULL`, categories and order are taken from the observed data.
`position`	Name of the columns specifying the start and end of the position where the event occured on the protein. The column indicated as the end position should contain `NA` for point events and ending position for events spanning more than one position.
`pfam`	data.frame containing PFAM domain data, in the form of columns start, end, as well as label information (see pfamLabels)
`pfamLabels`	Name of the column in pfam which specifies labels for the domains to print in the image
`structPred`	data.frame containing secondary structure predictions. Should contain a column "start" which indicates position on the protein, as well as columns "helix", "strand", and "coil" representing estimated probabilities/confidence (on a scale of 0 to 10) of the respective structures at that point.
`hydro`	data.frame containing hydrophobicity data. Should contain a column "start" indicating position on the protein and "featureValue" indicating the estimated hydrophobicity at that position.
`transMem`	data.frame containing estimated positions of Transmembrane Domains. Should contain columns "start", and "end" indicating position of the domain, as well as an optional column "featureType" indicating the process used to perform the prediction
`sigP`	data.frame containing the estimated position of the signal peptide. Should contain columns "start" and "end" indicating position on the protein.
`xlim`	Numeric. Indicates range of possible amino acid positions. Eg c(1, 857).
`tmposcol`	Column names in transMem indicating start and end of domain position.
`main`	Main title for the entire visualization.
`logscale`	Logical. If TRUE heights of count bars are in capped log scale. Defaults to TRUE
`logbase`	Numeric. Indicates the base of the log to use if logscale = TRUE. Ignored if logscale=FALSE. Defaults to 1.506.
`scale.factor`	Numeric. Indicates maximum height of a bar (for values to be compared against). Defaults to 10.
`colpalette`	Color palette to use in the counting portion of the plot. Color is used to indicate relative frequency. Should be a character vector containing hex color specifications.
`legend.step`	Numeric. Step size used to differentiate between colors in colpalette.
`sampleID`	Character. Column name in events which indicates unique sample identifier. Used to determine total sample size in a given category.
`subtitle`	Character. Subtitle for the entire visualization. Appears below the image.
`draw`	Logical. Should the plot be drawn to the active graphics device. Defaults to FALSE. If FALSE a trellis object representing the visualization is returned.
`vertGuides`	Integer. Number of vertical guidelines to draw in the images. Lines will be equally spaced.
`sequence.counts`	data.frame or NULL. Data.frame containing the total number of sequenced samples. This is necessary because not all samples will contain at least one variant, and thus would not appear in `events`. Should contain columns "category" and "count". Categories must match those which appear in `events` and `requiredCats` exactly. Categories with 0 counts but which appear in `requiredCats` must be included.
`metaFileName`	Character. Indicates location to save the svg of the metaCountStructPlot image.
`structFileName`	Character. Indicates location to save the svg of the proteinStructPlot image.
`metaHeight`	Numeric. Indicates height desired for variant/structure plot in inches.
`structHeight`	Numeric. Indicates height desired for structure only plot in inches.
`width`	Numeric. Indicates width desired for both plots in inches.

In the case of proteinStructPlot and metaCountStructPlot a complex image is generate based on the inputs. A trellis object is returned describing the plot, after being drawn or not as indicated by draw.

In the case of createProteinImages, two interactive svg images are created and saved to the harddrive at the locations specified in metaFileName and structFileName. The return value for this function is not meaningful.

Gabriel Becker

gmbecker/ProteinVis documentation built on May 17, 2019, 6:42 a.m.