Nothing
## ---- eval=FALSE--------------------------------------------------------------
# if (!requireNamespace("BiocManager", quietly=TRUE))
# install.packages("BiocManager")
# BiocManager::install("TnT")
## ---- eval=FALSE--------------------------------------------------------------
# devtools::install_github("marlin-na/TnT")
## -----------------------------------------------------------------------------
suppressPackageStartupMessages(library(TnT))
## -----------------------------------------------------------------------------
gr <- GenomicRanges::GRanges("chr7",
ranges = IRanges(
start = c(26549019L, 26564119L, 26585667L, 26591772L, 26594192L, 26623835L,
26659284L, 26721294L, 26821518L, 26991322L),
end = c(26550183L, 26564500L, 26586158L, 26593309L, 26594570L, 26624150L,
26660352L, 26721717L, 26823297L, 26991841L)),
ID = 1:10,
Name = paste("My Range", 1:10)
)
btrack <- TnT::BlockTrack(gr)
btrack
## -----------------------------------------------------------------------------
args(TnT::BlockTrack)
## -----------------------------------------------------------------------------
TnT::TnTGenome(btrack)
## ---- echo=FALSE--------------------------------------------------------------
df <- data.frame(stringsAsFactors = FALSE,
Constructor = c("BlockTrack", "VlineTrack", "PinTrack", "LineTrack", "AreaTrack",
"GeneTrackFromTxDb", "FeatureTrack", "GroupFeatureTrack",
"TxTrackFromTxDb", "TxTrackFromGRanges", "merge")
)
map.source <- c(
BlockTrack = "GRanges",
FeatureTrack = "GRanges",
VlineTrack = "Width-one GRanges",
PinTrack = "Width-one GRanges paired with values",
LineTrack = "Width-one GRanges paired with values",
AreaTrack = "Width-one GRanges paired with values",
GeneTrackFromTxDb = "TxDb",
TxTrackFromTxDb = "TxDb",
TxTrackFromGRanges = "GRanges paired with 'type' and 'tx_id'",
GroupFeatureTrack = "GRangesList",
merge = "Two or more tracks"
)
map.feature <- c(
BlockTrack = "block",
VlineTrack = "vline",
PinTrack = "pin",
LineTrack = "line",
AreaTrack = "area",
GeneTrackFromTxDb = "gene",
FeatureTrack = "gene",
GroupFeatureTrack = "tx",
TxTrackFromTxDb = "tx",
TxTrackFromGRanges = "tx",
merge = "composite"
)
map.link <- list(
BlockTrack = c("Block Track" = "tracktype-BlockTrack.html"),
VlineTrack = c("Vline Track" = "tracktype-VlineTrack.html"),
PinTrack = c("Pin Track" = "tracktype-PinTrack.html"),
LineTrack = c("Line and Area Track" = "tracktype-LineTrack-AreaTrack.html"),
AreaTrack = c("Line and Area Track" = "tracktype-LineTrack-AreaTrack.html"),
GeneTrackFromTxDb = c("Gene Track and Feature Track" = "tracktype-GeneTrack.html"),
FeatureTrack = c("Gene Track and Feature Track" = "tracktype-GeneTrack.html"),
GroupFeatureTrack = c("Tx Track and GroupFeatureTrack" = "tracktype-TxTrack.html"),
TxTrackFromTxDb = c("Tx Track and GroupFeatureTrack" = "tracktype-TxTrack.html"),
TxTrackFromGRanges = c("Tx Track and GroupFeatureTrack" = "tracktype-TxTrack.html"),
merge = c("Composite Track" = "track-CompositeTrack.html")
)
genlink <- function (li.pairs) {
vapply(li.pairs, FUN.VALUE = character(1),
function (pairs) {
stopifnot(length(pairs) == 1)
name <- names(pairs)
base.link <- unname(pairs)
sprintf("[%s](http://tnt.marlin.pub/articles/examples/%s)", name, base.link)
}
)
}
df$Source <- map.source[df$Constructor]
df$`Feature type` <- map.feature[df$Constructor]
df$`Example` <- genlink(map.link[df$Constructor])
knitr::kable(df)
## -----------------------------------------------------------------------------
TnT::trackSpec(btrack, "background")
btrack2 <- btrack
TnT::trackSpec(btrack2, "background") <- "blanchedalmond"
TnT::trackSpec(btrack2, "label") <- "My Ranges"
TnT::trackSpec(btrack2, "height") <- 50
## -----------------------------------------------------------------------------
btrack2$color # Equivalent to `trackData(btrack2)$color`
btrack2$color <- "darkseagreen4" # Equivalent to `trackData(btrack2)$color <- "darkseagreen4"`
## -----------------------------------------------------------------------------
TnT::trackData(btrack2) <- GenomicRanges::shift(TnT::trackData(btrack2), 10000)
## -----------------------------------------------------------------------------
TnT::TnTBoard(list(btrack, btrack2))
## -----------------------------------------------------------------------------
TnT::tooltip(btrack2) <- cbind(TnT::tooltip(btrack2),
as.data.frame(TnT::trackData(btrack2)))
TnT::TnTGenome(btrack2, view.range = TnT::trackData(btrack2)[4] * .05)
## -----------------------------------------------------------------------------
set.seed(6)
pintrack <- TnT::PinTrack(GRanges("chr7", IRanges(start = sample(26300000:27000000, 4), width = 1)),
value = c(1,3,2,4), color = c("blue", "yellow", "green", "red"))
TnT::TnTGenome(
list(pintrack, btrack2),
view.range = GRanges("chr7", IRanges(26550000, 26600000)),
coord.range = IRanges(26350000, 27050000),
zoom.allow = IRanges(50000, 200000)
)
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