chromPlot: Global visualization tool of genomic data

Description

Package designed to visualize genomic data along the chromosomes, where the vertical chromosomes are sorted by number, with sex chromosomes at the end.

Usage

chromPlot(annot1, annot2, annot3, annot4, stat, stat2, 
scale.title="Counts", statTyp="p", scex=1, spty=20, statCol, statCol2,
statName="Statistic", statName2="Statistic2", bands, bandsDesc, gaps,
gapsDesc, segment, segmentDesc, segment2=NULL, segment2Desc=NULL, chr,
bin=1e6, yAxis=TRUE, figCols=NULL, colBand="lightgray", colAnnot1="brown", 
colAnnot2="gold", colAnnot3="darkgreen", colAnnot4="blue", colSegments=c("darkgreen",
"orange", "blue",  "darkslategray2", "cyan", "blueviolet", "goldenrod3", "darkseagreen4",
"red", "green", "salmon", "darkolivegreen", "maroon", "purple"), 
colSegments2=colSegments[-1L], colStat="blue", colStat2="orange", title=NULL,
plotRndchr=FALSE, maxSegs=200, noHist=FALSE, segLwd=3, sortSegs=TRUE,
chrSide=c(-1, -1, -1, -1, 1, 1, -1, 1), cex=0.75, legChrom, org=NULL, strand=NULL,
stack=TRUE, statThreshold=NULL, statThreshold2=NULL, statSumm="none")

Arguments

annot1

Genome annotations

annot2

Genome annotations, subset of annot1

annot3

Genome annotations, subset of annot2

annot4

Genome annotations, subset of annot3

stat

Genome annotations associated to quantitative values

stat2

Second track of genome annotations associated to quantitative values

statCol

Name column in stat with the values to plot

statCol2

Name column in stat2 with the values to plot

statTyp

Type of plot for stat ("l", "p", NULL)

statName

Description for stat (default="Statistic")

statName2

Description for stat2 (default="Statistic")

bands

Genome annotations to be plotted on chromosomal body (e.g G bands)

bandsDesc

Description for bands

gaps

Chromosome alignment gaps (only centromers and telomers used)

gapsDesc

Description for gaps

segment

Genomic segments. Can contain a 'Group' column with categories

segmentDesc

Description for segment

segment2

second track of genomic segments. Can contain a 'Group' column with categories

segment2Desc

Description for segment2

chr

Vector of chromosome names to plotted (optional)

bin

Bin size for histograms in base pairs

yAxis

Should I draw the y-axis (logical)

figCols

Maximum number of chromosomes in a row

colBand

Color for chromosome bands

colAnnot1

Color for histograms for annot1

colAnnot2

Color for histograms for annot2

colAnnot3

Color for histograms for annot3

colAnnot4

Color for histograms for annot4

colSegments

Color for chromosome segment (ignored if segment are grouped (see details)

colSegments2

Color for chromosome segment2 (ignored if segment2 are grouped (See details)

colStat

Color for stat

colStat2

Color for stat2

title

Plot title

plotRndchr

Include random scaffolds

maxSegs

Maximum number of segments. If the segment or segment2 tracks contain more segments than this value, a histogram of segments is drawn instead

noHist

If TRUE, segments are never drawn as histograms, even they are more than maxSegs or if the largest segment is smaller than the bin size.

segLwd

Line width for segments

sortSegs

Sort overlapping segments by size

chrSide

Chromosome side where to draw annot1, annot2, annot3, annot4, segments, segments2, stat and stat2, respectively. 1=right, -1=left

cex

Cex for plot (see ?par for details)

legChrom

Legend chromosome (character string). Place legend after this chromosome

scale.title

Title for histograms scales

scex

Cex for stat track

spty

A character specifying the type of plot region to be used in stat

org

Organism name, e.g. mmusculus, hsapiens

strand

Strand "+" or "-" for local view using GenomeGraphs

stack

Stack overlapping segments in segment and segment2 in clusters

statThreshold

Only plot segments in stat with values above this threshold

statThreshold2

Only plot segments in stat2 with values above this threshold

statSumm

Type of statistical function for apply to the data ("mean", "median","sum", "none"), if the value is 'none', chromPlot will not apply some statistical function.

Value

Karyotype diagram in device.

Details

chromPlot package creates an idiogram with all chromosomes including the sex chromosomes. The package is able to plot genomic data on both sides of chromosome as histograms or vertical segments. Histograms represent the number of genomic elements in each bin of size bin. The parameters annot1, annot2, annot3, annot4, segment, segment2, stat, stat2, band, gaps should be data.frames with at leas these columns: 'Chrom', 'Start', 'End'. The gaps and bands arguments are used to plot the chromosomal ideogram.The argument band should also have a 'Group' column with categories for classifying each annotation element. Arguments stat and stat2 should have a statCol and stat2Col column respectively with continuoos values.

If plotted on the same chromosomal side, tracks will be plotted on top of each other, in the order they are in the function's syntax. This can be used for plotting stacked barplots if, for instance, annot1, annot2, annot3, and annot4 are supersets of ecah other. This, however, is not enforced nor checked. An alternative way to create a stacked histogram is providing a single track with Group category. The user can modify the side tracks are plotted on by modifying chrSide.

The segment and segment2 tracks are plotted as vertical bars by default. However, the their elements exceed in number given to maxSegs or if the maximum segment size is smaller than bin, they are plotted as histograms. This behaviour can be modified by setting noHist = TRUE.

For more details and usage examples see the vignette.

Examples

Run this code

data(hg_cytoBandIdeo)
data(hg_gap)
chromPlot(bands=hg_cytoBandIdeo, gaps=hg_gap)

Run the code above in your browser using DataLab