geom_alignment {ggbio} | R Documentation |
Show interval data as alignment.
## S4 method for signature 'GRanges' geom_alignment(data, ..., xlab, ylab, main, facets = NULL, stat = c("stepping", "identity"), range.geom = c("rect", "arrowrect"), gap.geom = c("chevron", "arrow", "segment"), rect.height = NULL, group.selfish = TRUE, label = TRUE) ## S4 method for signature 'TxDbOREnsDb' geom_alignment(data, ..., which, columns = c("tx_id", "tx_name", "gene_id"), names.expr = "tx_name", facets = NULL, truncate.gaps = FALSE, truncate.fun = NULL, ratio = 0.0025) ## S4 method for signature 'GRangesList' geom_alignment(data, ..., which = NULL, cds.rect.h = 0.25, exon.rect.h = cds.rect.h, utr.rect.h = cds.rect.h/2, xlab, ylab, main, facets = NULL, geom = "alignment", stat = c("identity", "reduce"), range.geom = "rect", gap.geom = "arrow", utr.geom = "rect", names.expr = NULL, label = TRUE, label.color = "gray40", arrow.rate = 0.015, length = unit(0.1, "cm")) ## S4 method for signature 'OrganismDb' geom_alignment(data, ..., which, columns = c("TXNAME", "SYMBOL", "TXID", "GENEID"), names.expr = "SYMBOL", facets = NULL, truncate.gaps = FALSE, truncate.fun = NULL, ratio = 0.0025 )
data |
A |
... |
Extra parameters such as aes() passed. |
which |
|
cds.rect.h |
cds heights. |
exon.rect.h |
exon heights. |
utr.rect.h |
utr heights. |
label.color |
label color. |
arrow.rate |
arrow rate. |
length |
arrow length. |
columns |
columns to get from object. |
xlab |
Label for x |
ylab |
Label for y |
main |
Title for plot. |
facets |
Faceting formula to use. |
stat |
For For |
gap.geom |
Geom for 'gap' computed from the data you passed based on the group information. |
rect.height |
Half height of the arrow body. |
group.selfish |
Passed to |
truncate.gaps |
logical value indicate to truncate gaps or not. |
truncate.fun |
shrinkage function. Please see |
ratio |
used in |
geom |
geometric object. only support "gene" now. |
range.geom |
geom for main intevals or exons. |
utr.geom |
geom for utr region. |
names.expr |
expression for showing y label. |
label |
logical value. Whether to label the intervals with names specified
by argument |
A 'Layer'.
Tengfei Yin
set.seed(1) N <- 100 require(GenomicRanges) ## ====================================================================== ## simmulated GRanges ## ====================================================================== gr <- GRanges(seqnames = sample(c("chr1", "chr2", "chr3"), size = N, replace = TRUE), IRanges( start = sample(1:300, size = N, replace = TRUE), width = sample(70:75, size = N,replace = TRUE)), strand = sample(c("+", "-", "*"), size = N, replace = TRUE), value = rnorm(N, 10, 3), score = rnorm(N, 100, 30), sample = sample(c("Normal", "Tumor"), size = N, replace = TRUE), pair = sample(letters, size = N, replace = TRUE)) ## ====================================================================== ## default ## ====================================================================== ggplot(gr) + geom_alignment() ## or ggplot() + geom_alignment(gr) ## ====================================================================== ## facetting and aesthetics ## ====================================================================== ggplot(gr) + geom_alignment(facets = sample ~ seqnames, aes(color = strand, fill = strand)) ## ====================================================================== ## stat:stepping ## ====================================================================== ggplot(gr) + geom_alignment(stat = "stepping", aes(group = pair)) ## ====================================================================== ## group.selfish controls when ## ====================================================================== ggplot(gr) + geom_alignment(stat = "stepping", aes(group = pair), group.selfish = FALSE) ## ======================================= ## main/gap geom ## ======================================= ggplot(gr) + geom_alignment(range.geom = "arrowrect", gap.geom = "chevron") ## ======================================= ## For TxDb ## ======================================= library(TxDb.Hsapiens.UCSC.hg19.knownGene) data(genesymbol, package = "biovizBase") txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene ## made a track comparing full/reduce stat. ggbio() + geom_alignment(data = txdb, which = genesymbol["RBM17"]) p1 <- ggplot(txdb) + geom_alignment(which = genesymbol["RBM17"]) p1 p2 <- ggplot(txdb) + geom_alignment(which = genesymbol["RBM17"], stat = "reduce") tracks(full = p1, reduce = p2, heights = c(3, 1)) tracks(full = p1, reduce = p2, heights = c(3, 1)) + theme_tracks_sunset() tracks(full = p1, reduce = p2, heights = c(3, 1)) + theme_tracks_sunset(axis.line.color = NA) ## change y labels ggplot(txdb) + geom_alignment(which = genesymbol["RBM17"], names.expr = "tx_id:::gene_id")