JunctionSeq Color Parameters

Description

This data set specifies some of the default color and style parameters for JunctionSeq. Any of these parameters can be overridden by using the colorList parameter in buildAllPlots, buildAllPlotsForGene, or plotJunctionSeqResultsForGene.

Usage

JUNCTIONSEQ.DEFAULT.COLOR.LIST

Format

A list.

Details

The parameter colorList must be a named list. Any elements with the names listed below will override the default JunctionSeq colors.

SIG.FEATURE.COLOR The color of vertical lines in the plotting panel, for significant features.

NOSIG.FEATURE.COLOR The color of vertical lines in the plotting panel, for tested but non-significant features.

UNTESTABLE.FEATURE.COLOR The color of vertical lines in the plotting panel, for untestable features.

EXCLUDED.FEATURE.COLOR The color of vertical lines in the plotting panel, for features that were not part of the analysis (for example: splice junctions in an exon-based analysis).

SIG.VERTLINE.COLOR, NOSIG.VERTLINE.COLOR, UNTESTABLE.VERTLINE.COLOR: The colors of the vertical dotted lines in the plotting panel.

SIG.FEATURE.BORDER.COLOR, NOSIG.FEATURE.BORDER.COLOR, UNTESTABLE.FEATURE.BORDER.COLOR, EXCLUDED.FEATURE.BORDER.COLOR: The color for borders of features in the gene and transcript annotation.

SIG.FEATURE.FILL.COLOR, NOSIG.FEATURE.FILL.COLOR, UNTESTABLE.FEATURE.FILL.COLOR, EXCLUDED.FEATURE.FILL.COLOR The colors for exon shading in the gene and transcript annotation.

KNOWN.SPLICE.LTY, NOVEL.SPLICE.LTY: These set the "lty" parameter for the known and novel splice junction diagrams. These must be specified as one of the character specifications. In other words, either a descriptive specification like "solid","dotted",etc., or by an even number of nonzero hexadecimal digits. See the section "Line Type Specification" in the graphical parameters help (linkpar). You CANNOT use the single-digit index specification, as this will fail when used in vector form with the others (technically you could use them, but only if you reset ALL lty parameters).

EXON.CONNECTION.LTY, NOVEL.SPLICE.CONNECTION.LTY, KNOWN.SPLICE.CONNECTION.LTY: The "lty" parameters for the lines that connect the features on the gene schematic diagram to the plotting panel. These have the same requirements as the previous set of lty parameters.

PLOTTING.LINE.COLORS Character vector. The colors for each condition, in order. Will be shortened to the number of conditions.

Value

See above.

Examples

data(exampleDataSet,package="JctSeqData");

#Set a few alternative colors:
buildAllPlotsForGene(geneID = "ENSRNOG00000009281", jscs, 
                     outfile.prefix = "./oddColors.",
                     colorList = list(SIG.FEATURE.COLOR = "red",
                                      SIG.FEATURE.FILL.COLOR = "green",
                                      NOSIG.FEATURE.FILL.COLOR = "blue"
                                      ));

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(JunctionSeq)
Loading required package: SummarizedExperiment
Loading required package: GenomicRanges
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/JunctionSeq/defaultColorList.Rd_%03d_medium.png", width=480, height=480)
> ### Name: defaultColorList
> ### Title: JunctionSeq Color Parameters
> ### Aliases: JUNCTIONSEQ.DEFAULT.COLOR.LIST defaultColorList
> ###   junctionSeqColors
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(exampleDataSet,package="JctSeqData");
> 
> #Set a few alternative colors:
> buildAllPlotsForGene(geneID = "ENSRNOG00000009281", jscs, 
+                      outfile.prefix = "./oddColors.",
+                      colorList = list(SIG.FEATURE.COLOR = "red",
+                                       SIG.FEATURE.FILL.COLOR = "green",
+                                       NOSIG.FEATURE.FILL.COLOR = "blue"
+                                       ));
starting buildAllPlotsForGene() for geneID: ENSRNOG00000009281
Starting nested heights...
Starting device: png (./oddColors.ENSRNOG00000009281-expr-TX.png)
> pJSRfG(): ENSRNOG00000009281, plot.type: expr (with TX)
Starting device: png (./oddColors.ENSRNOG00000009281-expr.png)
> pJSRfG(): ENSRNOG00000009281, plot.type: expr
Starting device: png (./oddColors.ENSRNOG00000009281-normCts-TX.png)
> pJSRfG(): ENSRNOG00000009281, plot.type: normCounts (with TX)
Starting device: png (./oddColors.ENSRNOG00000009281-normCts.png)
> pJSRfG(): ENSRNOG00000009281, plot.type: normCounts
Starting device: png (./oddColors.ENSRNOG00000009281-rExpr-TX.png)
> pJSRfG(): ENSRNOG00000009281, plot.type: rExpr (with TX)
Starting device: png (./oddColors.ENSRNOG00000009281-rExpr.png)
> pJSRfG(): ENSRNOG00000009281, plot.type: rExpr
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>