igvParam {tracktables} | R Documentation |
Use igvParam( object)) to create a parameter object to control IGV display invoked from maketracktable() report or from makeIGVSession() XML files. Parameters for bigwig, bam and intervals files may be provided. See IGV manual for a full description of options.
igvParam(bigwig.altColor = "darkgrey", bigwig.color = "darkgrey", bigwig.autoScale = "true", bigwig.displayMode = "COLLAPSED", bigwig.featureVisibilityWindow = -1, bigwig.fontSize = 10, bigwig.normalize = "false", bigwig.renderer = "BAR_CHART", bigwig.sortable = "true", bigwig.visible = "true", bigwig.windowFunction = "mean", bigwig.baseline = 0, bigwig.drawBaseline = "true", bigwig.flipAxis = "false", bigwig.maximum = 50, bigwig.minimum = 0, bigwig.type = "LINEAR", interval.altColor = "darkgrey", interval.color = "darkgrey", interval.autoScale = "true", interval.displayMode = "character", interval.featureVisibilityWindow = -1, interval.fontSize = 10, interval.height = 40, interval.normalize = "false", interval.renderer = "BASIC_FEATURE", interval.sortable = "true", interval.visible = "true", interval.windowFunction = "count", bam.altColor = "darkgrey", bam.color = "darkgrey", bam.autoScale = "true", bam.displayMode = "EXPANDED", bam.featureVisibilityWindow = -1, bam.fontSize = 10, bam.showSpliceJunctions = "false", bam.colorByTag = "", bam.colorOption = "UNEXPECTED_PAIR", bam.flagUnmappedPairs = "false", bam.groupByTag = "", bam.maxInsertSize = 1000, bam.minInsertSize = 50, bam.shadeBasesOption = "QUALITY", bam.shadeCenters = "true", bam.showAllBases = "false", bam.sortByTag = "") igvParam(bigwig.altColor = "darkgrey", bigwig.color = "darkgrey", bigwig.autoScale = "true", bigwig.displayMode = "COLLAPSED", bigwig.featureVisibilityWindow = -1, bigwig.fontSize = 10, bigwig.normalize = "false", bigwig.renderer = "BAR_CHART", bigwig.sortable = "true", bigwig.visible = "true", bigwig.windowFunction = "mean", bigwig.baseline = 0, bigwig.drawBaseline = "true", bigwig.flipAxis = "false", bigwig.maximum = 50, bigwig.minimum = 0, bigwig.type = "LINEAR", interval.altColor = "darkgrey", interval.color = "darkgrey", interval.autoScale = "true", interval.displayMode = "character", interval.featureVisibilityWindow = -1, interval.fontSize = 10, interval.height = 40, interval.normalize = "false", interval.renderer = "BASIC_FEATURE", interval.sortable = "true", interval.visible = "true", interval.windowFunction = "count", bam.altColor = "darkgrey", bam.color = "darkgrey", bam.autoScale = "true", bam.displayMode = "EXPANDED", bam.featureVisibilityWindow = -1, bam.fontSize = 10, bam.showSpliceJunctions = "false", bam.colorByTag = "", bam.colorOption = "UNEXPECTED_PAIR", bam.flagUnmappedPairs = "false", bam.groupByTag = "", bam.maxInsertSize = 1000, bam.minInsertSize = 50, bam.shadeBasesOption = "QUALITY", bam.shadeCenters = "true", bam.showAllBases = "false", bam.sortByTag = "")
bigwig.altColor |
A character vector of alternate colour for bigwigs displayed in IGV. |
bigwig.color |
A character vector of main colour for bigwigs displayed in IGV. |
bigwig.displayMode |
A character vector of display mode for bigwigs displayed in IGV. |
bigwig.featureVisibilityWindow |
A numeric vector of feature visibility window for bigwigs displayed in IGV (Defaut -1). |
bigwig.fontSize |
A numeric vector of font size for bigwigs displayed in IGV. |
bigwig.autoScale |
A character vector ("true"/"false") to indicate whether data is autoscaled for bigwigs displayed in IGV (Default "true"). |
bigwig.normalize |
A character vector ("true"/"false") to indicate whether data is normalised for bigwigs displayed in IGV (Default "false"). |
bigwig.renderer |
A character vector of renderer for bigwigs displayed in IGV (Default "BAR_CHART"). |
bigwig.sortable |
A character vector ("true"/"false") to indicate whether data is sortable for bigwigs displayed in IGV (Default "true"). |
bigwig.visible |
A character vector ("true"/"false") to indicate whether data is visible for bigwigs displayed in IGV (Default "true"). |
bigwig.windowFunction |
A character vector ("true"/"false") of window function for bigwigs displayed in IGV (Default "mean"). |
bigwig.baseline |
A numeric vector of baseline bigwigs displayed in IGV. |
bigwig.drawBaseline |
A character vector ("true"/"false") of whether to draw baseline for bigwigs displayed in IGV (Default "true"). |
bigwig.flipAxis |
A character vector ("true"/"false") to indicate whether to flip axis for bigwigs displayed in IGV (Default "false"). |
bigwig.maximum |
A numeric vector of maximum value to display for bigwigs displayed in IGV (Default 50). |
bigwig.minimum |
A numeric vector of minimum value to display for bigwigs displayed in IGV (Default 0). |
bigwig.type |
A character vector of display type for bigwigs displayed in IGV (Default "LINEAR"). |
interval.altColor |
A character vector of alternate colour for intervals displayed in IGV. |
interval.color |
A character vector of main colour for intervals displayed in IGV. |
interval.autoScale |
A character vector ("true"/"false") to indicate whether data is autoscaled for intervals displayed in IGV (Default "false"). |
interval.displayMode |
A character vector of display mode for intervals displayed in IGV (Default "COLLAPSED"). |
interval.featureVisibilityWindow |
A numeric vector of feature visibility window for intervals displayed in IGV (Defaut -1). |
interval.fontSize |
A numeric vector of font size for intervals displayed in IGV. |
interval.height |
A numeric vector of height for intervals displayed in IGV. |
interval.normalize |
A character vector ("true"/"false") to indicate whether data is normalised for intervals displayed in IGV (Default "false"). |
interval.renderer |
A character vector of renderer for intervals displayed in IGV (Default "BASIC_FEATURE"). |
interval.sortable |
A character vector ("true"/"false") to indicate whether data is sortable for intervals displayed in IGV (Default "true"). |
interval.visible |
A character vector ("true"/"false") to indicate whether data is visible for intervals displayed in IGV (Default "true"). |
interval.windowFunction |
A character vector ("true"/"false") of window function for intervals displayed in IGV (Default "count"). |
bam.altColor |
A character vector of alternate colour for bam files displayed in IGV. |
bam.color |
A character vector of main colour for bam files displayed in IGV. |
bam.autoScale |
A character vector ("true"/"false") to indicate whether data is autoscaled for bam files displayed in IGV (Default "false"). |
bam.displayMode |
A character vector of display mode for bam files displayed in IGV (Default "EXPANDED"). |
bam.featureVisibilityWindow |
A numeric vector of feature visibility window for bam files displayed in IGV (Defaut -1). |
bam.fontSize |
A numeric vector of font size for intervals displayed in IGV. |
bam.showSpliceJunctions |
A character vector ("true"/"false") to indicate whether to show splice juntions for bam files displayed in IGV (Default "false"). |
bam.colorByTag |
A character vector to indicate whether to colour reads by Tags for Bam files (Defualt = ""). |
bam.colorOption |
A character vector of option to highlight Tags for Bam files (Defualt = "UNEXPECTED_PAIR"). |
bam.flagUnmappedPairs |
A character vector ("true"/"false") to indicate whether to flaf unmapped pairs for bam files displayed in IGV (Default "false"). |
bam.groupByTag |
A character vector ("true"/"false") to indicate how to groups reads by Tag for bam files displayed in IGV (Default ""). |
bam.maxInsertSize |
A numeric vector of maximum insert size to display for Bam files. |
bam.minInsertSize |
A numeric vector of minimum insert size to display for Bam files. |
bam.shadeBasesOption |
A character vector of option to shade bases for Bam files (Default "QUALITY"). |
bam.shadeCenters |
A character vector ("true"/"false") to indicate whether to shade centres for bam files displayed in IGV (Default "false"). |
bam.showAllBases |
A character vector ("true"/"false") to indicate to show all bases for bam files displayed in IGV (Default "false"). |
bam.sortByTag |
A character vector ("true"/"false") to indicate how to sort reads by Tag for bam files displayed in IGV (Default ""). |
An igvParam class object to use with maketracktable,MakeIGVSession and makeIGVSessionMXL
Thomas Carroll
## Simple initialisation of an IGVParam object igvDisplayParams <- igvParam() ## More custom initialisation of an IGVParam object . igvDisplayParams <- igvParam(bigwig.color="red",bigwig.autoScale = "false", bigwig.minimum = 10,bigwig.maximum = 100) # See full parameters and IGV online manual for more details on customistions ## Use igvParams with maketracktables function to customise bigwig display colour and data range. fileLocations <- system.file("extdata",package="tracktables") bigwigs <- dir(fileLocations,pattern="*.bw",full.names=TRUE) intervals <- dir(fileLocations,pattern="*.bed",full.names=TRUE) bigWigMat <- cbind(gsub("_Example.bw","",basename(bigwigs)), bigwigs) intervalsMat <- cbind(gsub("_Peaks.bed","",basename(intervals)), intervals) fileSheet <- merge(bigWigMat,intervalsMat,all=TRUE) fileSheet <- as.matrix(cbind(fileSheet,NA)) colnames(fileSheet) <- c("SampleName","bigwig","interval","bam") SampleSheet <- cbind(as.vector(fileSheet[,"SampleName"]), c("EBF","H3K4me3","H3K9ac","RNAPol2"), c("ProB","ProB","ProB","ProB")) colnames(SampleSheet) <- c("SampleName","Antibody","Species") MakeIGVSession(SampleSheet,fileSheet, igvdirectory=getwd(),"Example","mm9", igvParams=igvDisplayParams)