Plot Smoothed Sense/Anti-sense of Specified Chromosomes

Description

For a given chromosome, plot the smooths of the sense and the anti-sense from 5' to 3' (left to right on x-axis).

Usage

plotChr(chrN, senseObj, cols = rep("black", length(senseObj[[1]])), log = FALSE, xloc = c("equispaced", "physical"), geneSymbols = FALSE, ngenes = 20, lines.at = NULL, lines.col = "red")

Arguments

Author(s)

Robert Gentleman and Xiaochun Li

See Also

Makesense

Examples

example(Makesense)

if (interactive())
  op <- par(ask=TRUE)

cols <- ifelse(expressionSet133a$cov1=="test 1", "red", "green")
plotChr("21", esetobj, cols)

# plot on log-scale:

plotChr("21", esetobj, cols, log=TRUE)

# genesymbol instead of probe names:

plotChr("21", esetobj, cols, log=TRUE, geneSymbols=TRUE)

# add vertical lines at genes of interest:

gs <- c("220372_at", "35776_at", "200943_at")
plotChr("21", esetobj, cols, log=TRUE, geneSymbols=FALSE, lines.at=gs)

# add vertical lines at genes of interest
# with specified colors:

gs <- c("220372_at", "35776_at", "200943_at")
cc <- c("blue", "cyan","magenta")
plotChr("21", esetobj, cols, log=TRUE, geneSymbols=FALSE, lines.at=gs,
lines.col=cc)
if (interactive())
  par(op)

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)

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Type 'demo()' for some demos, 'help()' for on-line help, or
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> library(geneplotter)
Loading required package: Biobase
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

Welcome to Bioconductor

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

Loading required package: lattice
Loading required package: annotate
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: XML
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/geneplotter/plotChr.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plotChr
> ### Title: Plot Smoothed Sense/Anti-sense of Specified Chromosomes
> ### Aliases: plotChr
> ### Keywords: hplot
> 
> ### ** Examples
> 
> example(Makesense)

Maksns>   if (require("hgu133a.db")) {
Maksns+     data(expressionSet133a)
Maksns+     esetobj <- Makesense(exprs(expressionSet133a), "hgu133a")
Maksns+     esetobj2 <- Makesense(expressionSet133a[1:200, ])
Maksns+   }
Loading required package: hgu133a.db
Loading required package: org.Hs.eg.db


> 
> #if (interactive())
>   op <- par(ask=TRUE)
> 
> cols <- ifelse(expressionSet133a$cov1=="test 1", "red", "green")
> plotChr("21", esetobj, cols)
> 
> # plot on log-scale:
> 
> plotChr("21", esetobj, cols, log=TRUE)
Warning messages:
1: In log(-smooths$neg$y) : NaNs produced
2: In log(-smooths$neg$y) : NaNs produced
3: In log(-smooths$neg$y) : NaNs produced
4: In log(-smooths$neg$y) : NaNs produced
5: In log(smooths$pos$y) : NaNs produced
> 
> # genesymbol instead of probe names:
> 
> plotChr("21", esetobj, cols, log=TRUE, geneSymbols=TRUE)
Warning messages:
1: In log(-smooths$neg$y) : NaNs produced
2: In log(-smooths$neg$y) : NaNs produced
3: In log(-smooths$neg$y) : NaNs produced
4: In log(-smooths$neg$y) : NaNs produced
5: In log(smooths$pos$y) : NaNs produced
> 
> # add vertical lines at genes of interest:
> 
> gs <- c("220372_at", "35776_at", "200943_at")
> plotChr("21", esetobj, cols, log=TRUE, geneSymbols=FALSE, lines.at=gs)
Warning messages:
1: In log(-smooths$neg$y) : NaNs produced
2: In log(-smooths$neg$y) : NaNs produced
3: In log(-smooths$neg$y) : NaNs produced
4: In log(-smooths$neg$y) : NaNs produced
5: In log(smooths$pos$y) : NaNs produced
> 
> # add vertical lines at genes of interest
> # with specified colors:
> 
> gs <- c("220372_at", "35776_at", "200943_at")
> cc <- c("blue", "cyan","magenta")
> plotChr("21", esetobj, cols, log=TRUE, geneSymbols=FALSE, lines.at=gs,
+ lines.col=cc)
Warning messages:
1: In log(-smooths$neg$y) : NaNs produced
2: In log(-smooths$neg$y) : NaNs produced
3: In log(-smooths$neg$y) : NaNs produced
4: In log(-smooths$neg$y) : NaNs produced
5: In log(smooths$pos$y) : NaNs produced
> #if (interactive())
>   par(op)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>