dandelion.plot {trackViewer} | R Documentation |
Plot variants and somatic mutations
dandelion.plot(SNP.gr, features = NULL, ranges = NULL, type = c("fan", "circle", "pie", "pin"), newpage = TRUE, ylab = TRUE, xaxis = TRUE, yaxis = FALSE, legend = NULL, cex = 1, maxgaps = 1/50, heightMethod = NULL, ...)
SNP.gr |
A object of GRanges or GRangesList. All the width of GRanges must be 1. |
features |
A object of GRanges or GRangesList. |
ranges |
A object of GRanges or GRangesList. |
type |
Character. Could be fan, circle, pie or pin. |
newpage |
plot in the new page or not. |
ylab |
plot ylab or not. If it is a character vector, the vector will be used as ylab. |
xaxis, yaxis |
plot xaxis/yaxis or not. If it is a numeric vector with length greater than 1, the vector will be used as the points at which tick-marks are to be drawn. And the names of the vector will be used to as labels to be placed at the tick points if it has names. |
legend |
If it is a list with named color vectors, a legend will be added. |
cex |
cex will control the size of circle. |
maxgaps |
maxgaps between the stem of dandelions. It is calculated by the width of plot region devided by maxgaps. If a GRanges object is set, the dandelions stem will be clusted in each genomic range. |
heightMethod |
A function used to determine the height of stem of dandelion. eg. Mean. Default is length. |
... |
not used. |
In SNP.gr and features, metadata of the GRanges object will be used to control thecolor, fill, border, height, data source of pie if the type is pie.
SNP <- c(10, 100, 105, 108, 400, 410, 420, 600, 700, 805, 840, 1400, 1402) SNP.gr <- GRanges("chr1", IRanges(SNP, width=1, names=paste0("snp", SNP)), score=sample.int(100, length(SNP))/100) features <- GRanges("chr1", IRanges(c(1, 501, 1001), width=c(120, 500, 405), names=paste0("block", 1:3)), color="black", fill=c("#FF8833", "#51C6E6", "#DFA32D"), height=c(0.1, 0.05, 0.08)) dandelion.plot(SNP.gr, features, type="fan")