stat_aggregate {ggbio} | R Documentation |
Generates summaries on the specified windows
## S4 method for signature 'GRanges' stat_aggregate(data, ..., xlab, ylab, main, by, FUN, maxgap=-1L, minoverlap=0L, type=c("any", "start", "end", "within", "equal"), select=c("all", "first", "last", "arbitrary"), y = NULL, window = NULL, facets = NULL, method = c("mean", "median","max", "min", "sum", "count", "identity"), geom = NULL)
data |
A |
... |
Arguments passed to plot function. such as aes() and color. |
xlab |
Label for x |
ylab |
Label for y |
main |
Title for plot. |
by |
An object with 'start', 'end', and 'width' methods. Passed to |
FUN |
The function, found via 'match.fun', to be applied to each window of
'x'. Passed to |
maxgap, minoverlap, type |
Used in the internal call to |
select |
It passed to When If |
y |
A character indicate the varialbe column for which aggregation is taken on, same as aes(y = ). |
window |
Integer value indicate window size. |
facets |
Faceting formula to use. |
method |
customized method for aggregating, if FUN is not provided. |
geom |
The geometric object to use display the data. |
A 'Layer'.
Tengfei Yin
library(GenomicRanges) set.seed(1) N <- 1000 ## ====================================================================== ## 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)) ggplot(gr) + stat_aggregate(aes(y = value)) ## or ## ggplot(gr) + stat_aggregate(y = "value") ggplot(gr) + stat_aggregate(aes(y = value), window = 36) ggplot(gr) + stat_aggregate(aes(y = value), select = "first") ## Not run: ## no hits ggplot(gr) + stat_aggregate(aes(y = value), select = "first", type = "within") ## End(Not run) ggplot(gr) + stat_aggregate(window = 30, aes(y = value),fill = "gray40", geom = "bar") ggplot(gr) + stat_aggregate(window = 100, fill = "gray40", aes(y = value), method = "max", geom = "bar") ggplot(gr) + stat_aggregate(aes(y = value), geom = "boxplot") ggplot(gr) + stat_aggregate(aes(y = value), geom = "boxplot", window = 60) ## now facets need to take place inside stat_* geom_* for an accurate computation ggplot(gr) + stat_aggregate(aes(y = value), geom = "boxplot", window = 30, facets = sample ~ seqnames) ## FIXME: ## autoplot(gr, stat = "aggregate", aes(y = value), window = 36) ## autoplot(gr, stat = "aggregate", geom = "boxplot", aes(y = value), window = 36)