## ---------------------------------------------------------------------------------------------------------------------------------＃if（！sireseenamespace（“ biocmanager”，悄悄= true））＃install.packages（“ biocmanager”）＃biocmanager ::安装（“ tnt”）## --------------------------------------------------------------------------------------------------------------------------------------------------------------------------＃DevTools :: install_github（“ Marlin-Na/tnt”）## -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------抑制PackagestartupMessages（库（TNT））## ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ gr <-genomicranges :: granges（“ chr7”，ranges = iranges（start = c（26549019L，26564119L，26585667L，26591772L，26594192L26550183L，26564500L，26586158L，26593309L，26594570L，26624150L，26660352L，26721717L，26823297L，26823297L，269991841L），26991841L），IDgr）btrack ## --------------------------------------------------------------------------------------------------------------------------------------------------------------------LockTrack）## --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- TnT::TnTGenome(btrack) ## ---- echo=FALSE---------------------------------------------------------------------------------------------------------------- data.frame（stringsasFactors = false，constructor = c（“ blockTrack”，“ vlinetrack”，“ pintrack”，“ linetrack”，“ airtrack”，“ genetrackfromtxdb”，“ farterUretrack”“，” groupFeatUretrack”，“ txtrackfromtxdb”，“ txtrackfromgranges”，“ Merge”））Map.Source <-C（BlockTrack =“ Granges”，farterurotrack =“ granges”，vlinetrack =“ vlinetrack =“ width-one granges granges granges”，pintrack =“”，pintrack =“”，宽度一granges与“ linetrack =” width-One Granges配对，与值配对”，airtrack =“ width-One Granges与值配对”，Genetrackfromtxdb =“ txdb”，txtrackfromtxdb =“ 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) )