plotBedgraph {Sushi} | R Documentation |
plots data stored in bed file format
plotBedgraph(signal, chrom, chromstart, chromend, range = NULL, color = SushiColors(2)(2)[1], lwd = 1, linecolor = NA, addscale = FALSE, overlay = FALSE, rescaleoverlay = FALSE, transparency = 1, flip = FALSE, xaxt = "none", yaxt = "none", xlab = "", ylab = "", xaxs = "i", yaxs = "i", bty = "n", ymax = 1.04, colorbycol = NULL, ...)
signal |
signal track data to be plotted (in bedgraph format) |
chrom |
chromosome of region to be plotted |
chromstart |
start position |
chromend |
end position |
range |
y-range to plpt ( c(min,max) ) |
color |
color of signal track |
lwd |
color of line outlining signal track. (only valid if linecol is not NA) |
linecolor |
color of line outlining signal track. use NA for no outline |
addscale |
TRUE/FALSE whether to add a y-axis |
overlay |
TRUE / FALSE whether this data should be plotted on top of an existing plot |
rescaleoverlay |
TRUE/FALSE whether the new plot shold be rescaled based on the maximum value to match the existing plot (only valid when overlay is set to 'TRUE') |
transparency |
Value between 0 and 1 indication the degree of transparency of the plot |
flip |
TRUE/FALSE whether the plot should be flipped over the x-axis |
xaxt |
A character which specifies the x axis type. See |
yaxt |
A character which specifies the y axis type. See |
xlab |
Label for the x-axis |
ylab |
Label for the y-axis |
xaxs |
Must be set to 'i' for appropriate integration into Sushi plots. See |
yaxs |
Must be set to 'i' for appropriate integration into Sushi plots. See |
bty |
A character string which determined the type of box which is drawn about plots. See |
ymax |
fraction of max y value to set as height of plot. |
colorbycol |
palette to use to shade the signal track plot. Only applicable when overlay is set to FALSE. |
... |
values to be passed to |
data(Sushi_ChIPSeq_CTCF.bedgraph) data(Sushi_DNaseI.bedgraph) chrom = "chr11" chromstart = 1955000 chromend = 1965000 plotBedgraph(Sushi_ChIPSeq_CTCF.bedgraph,chrom,chromstart,chromend,transparency=.50,flip=FALSE,color="blue",linecol="blue") plotBedgraph(Sushi_DNaseI.bedgraph,chrom,chromstart,chromend,transparency=.50,flip=FALSE,color="#E5001B",linecol="#E5001B",overlay=TRUE,rescaleoverlay=TRUE) labelgenome(chrom,chromstart,chromend,side=1,scipen=20,n=3,line=.18,chromline=.5,scaleline=0.5,scale="Mb") transparency = 0.5 col1 = col2rgb("blue") finalcolor1 = rgb(col1[1],col1[2],col1[3],alpha=transparency * 255,maxColorValue = 255) col2 = col2rgb("#E5001B") finalcolor2 = rgb(col2[1],col2[2],col2[3],alpha=transparency * 255,maxColorValue = 255) legend("topright",inset=0.025,legend=c("DnaseI","ChIP-seq (CTCF)"),fill=c(finalcolor1,finalcolor2),border=c("blue","#E5001B"),text.font=2,cex=0.75)