View source: R/RCircosPlotDataTracks.R
RCircos.Line.Plot | R Documentation |
Draw one track of continue lines which connect each neighbor data points. RCircos core components and graphics device must bae initialized before drawing.
RCircos.Line.Plot(line.data=NULL, data.col=4, track.num=NULL, side=c("in", "out"), min.value=NULL, max.value=NULL, inside.pos=NULL, outside.pos=NULL, genomic.columns=3, is.sorted=TRUE)
line.data |
A data frame with the first three columns for chromosome names, start and end position of each data point followed by data values for one or more samples. |
data.col |
Non-negative integer, representing the ordinal number of the column in input dataset that contains the data to be plotted. |
track.num |
Non-negative integer, representing the ordinal number of the plot track where the lines will be plotted. |
side |
Character vector, either "in" or "out", representing the position related to chromosome ideogram. |
min.value |
Numeric, minimum value of line data. |
max.value |
Numeric, maximum value of line data |
inside.pos |
Non-negative numeric, inside position (relative to the centre of plot area) of the track . |
outside.pos |
Non-negative numeric, outside position (relative to the centre of plot area) of the track. |
genomic.columns |
Non-negative integer, total number of columns for genomic position in each row. Must be either 3 or 2. |
is.sorted |
Logic, whether the data is sorted by chromosome names and start positions. |
Henry Zhang
## Not run: library(RCircos); data(UCSC.HG19.Human.CytoBandIdeogram); data(RCircos.Line.Data); RCircos.Set.Core.Components( cyto.info=UCSC.HG19.Human.CytoBandIdeogram, chr.exclude=c("chrX", "chrY"), num.inside=10, num.outside=0) RCircos.Set.Plot.Area() RCircos.Chromosome.Ideogram.Plot() RCircos.Line.Plot(RCircos.Line.Data, data.col=5, track.num=1, side="in") RCircos.Line.Plot(RCircos.Line.Data, data.col=5, side="in", inside.pos=1.5, outside.pos=1.75) ## End(Not run)
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