蒲公英的阴谋

有时，一个基因中涉及的SNPs多达数百个。蒲公英图可以用来描述如此密集的snp。请注意，蒲公英的高度表示snp的密度。

library(trackViewer) library(TxDb.Hsapiens.UCSC.hg19.knownGene) library(org.Hs.eg.db) library(rtracklayer) methy <- import(system. exe .db)文件(“extdata”、“甲基。bed"， package="trackViewer")， " bed") gr <- GRanges("chr22"， IRanges(50968014, 50970514, names="TYMP")) trs <- geneModelFromTxdb(TxDb.Hsapiens.UCSC.hg19. txt)。knownGene, org. hs . exe .db, gr=gr) features <- c(range(trs[[1]]$dat)， range(trs[[5]]$dat)) names(features) <- c(trs[[1]]$name, trs[[5]]$name) features$fill <- c("浅蓝色"，"mistyrose") features$height <- c(。02， .04)蒲公英。Plot (methy, features, ranges=gr, type="pin")

改变蒲公英的类型

蒲公英地块还有一种类型，即“扇子”类型。扇形的面积表示甲基化百分比或突变率。

methy$color <- 3 methy$border <- "gray" ##分数信息是必需的，分数必须是[0,1]m中的一个数字<- max(methy$ Score) methy$ Score <- methy$ Score /m蒲公英。Plot (methy, features, ranges=gr, type="fan")

Methy $color <- rep(list(c(3,5))， length(Methy)) Methy $score2 <- (max(Methy $score) - Methy $score)/m legends <- list(list(labels=c("s1"， "s2")， fill=c(3,5)))蒲公英。Plot (methy, features, ranges=gr, type="pie"， legend=legends)

改变蒲公英的数量

少些蒲公英。Plot (methy, features, ranges=gr, type="circle"， maxgaps=1/10)

更多蒲公英蒲公英。Plot (methy, features, ranges=gr, type="circle"， maxgaps=1/100)

用户还可以通过将maxgaps设置为GRanges对象来指定相邻蒲公英之间的最大距离。

Maxgaps <- tile(gr, n = 10)[[1]]蒲公英。Plot (methy, features, ranges=gr, type="circle"， maxgaps=maxgaps)

加上y轴(yaxis)

将yaxis设置为TRUE以添加y轴，并设置heightMethod＝的意思是用平均分作为高度。

蒲公英。plot(methy, features, ranges=gr, type="pie"， maxgaps=1/100, yaxis = TRUE, hightmethod = mean, ylab=' methy得分的平均值')

Yaxis = c(0,0.5, 1)蒲公英。plot(methy, features, ranges=gr, type="pie"， maxgaps=1/100, yaxis = yaxis, hightmethod = mean, ylab=' methy得分的平均值')

会话信息

sessionInfo ()

R版本4.2.1(2022-06-23)平台:x86_64-pc-linux-gnu(64位)运行在Ubuntu 20.04.4 LTS下

矩阵产品:默认BLAS: /home/biocbuild/bbs-3.16-bioc/R/lib/libRblas。so LAPACK: /home/biocbuild/bbs-3.16-bioc/R/lib/libRlapack.so

locale: [1] LC_CTYPE=en_US。utf - 8 LC_NUMERIC = C
[3] LC_TIME=en_GB LC_COLLATE=C
[5] LC_MONETARY = en_US。utf - 8LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER = en_US。utf - 8 LC_NAME = C
[9] lc_address = c lc_phone = c
[11] LC_MEASUREMENT = en_US。utf - 8 LC_IDENTIFICATION = C

附加的基本包:[1]grid stats4 stats graphics grDevices utils datasets[8]方法基础

其他附加包:[1]httr_1.4.3
[2] VariantAnnotation_1.43.2
[3] Rsamtools_2.13.3
[4] Biostrings_2.65.1
[5] XVector_0.37.0
[6] SummarizedExperiment_1.27.1
[7] MatrixGenerics_1.9.1
[8] matrixStats_0.62.0
[9] org.Hs.eg.db_3.15.0
[10] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2
[12] AnnotationDbi_1.59.1
[13] Biobase_2.57.1
[14] Gviz_1.41.1
[15] rtracklayer_1.57.0
[16] trackViewer_1.33.5
[17] Rcpp_1.0.9
[18] GenomicRanges_1.49.0
[19] GenomeInfoDb_1.33.3
[20] IRanges_2.31.0
[21] S4Vectors_0.35.1
[22] BiocGenerics_0.43.0

通过命名空间加载(且未附加):[1]colorspace_2.0-3 rjson_0.2.21 deldir_1.0-6
[4] ellipsis_0.3.2 biovizBase_1.45.0 htmlTable_2.4.1
[7] base64enc_0.1-3 dicchromat_2 .0-0.1 rstudioapi_0.13 . rstudioapi_0.13
[10] bit64_4.0.5 fansi_1.0.3 xml2_1.3.3 .
[13] codetools_0.2-18 splines_4.2.1 cachem_1.0.6
Formula_1.2-4 jsonlite_1.8.0
[19] cluster_2.1.3 dbplyr_2.2.1 png_0.1-7
[22] grImport_0.9-5 graph_1.75.0 BiocManager_1.30.18 .使用本文
[25] compiler_4.2.1 backports_1.4.1 lazyeval_0.2.2
matrix_1.4 .1 -1 fastmap_1.1.0
[31] cli_3.3.0 htmltools_0.5.3 prettyunits_1.1.1
[34] tools_4.2.1 gtable_0.3.0 glue_1.6.2
[37] GenomeInfoDbData_1.2.8 dplyr_1.0.9 rappdirs_0.3.3
[40] jquerylib_0.1.4 rhdf5filters_1.9.0 vctrs_0.4.1
[43] xfun_0.31 string_1 .4.0 lifecycle_1.0.1 .
[46] ensembldb_2.21.2 restfulr_0.0.15 InteractionSet_1.25.0
[49] XML_3.99-0.10 zlibbioc_1.43.0 scales_1.2.0
[52] BiocStyle_2.25.0 BSgenome_1.65.2 ProtGenerics_1.29.0 . [52] BiocStyle_2.25.0
[55] hms_1.1.1 parallel_4.2.1 rhdf5_2.41.1
[58] AnnotationFilter_1.21.0 RColorBrewer_1.1-3 yaml_2.3.5
[61] curl_4.3.2 memoise_2.0.1 gridExtra_2.3
[64] ggplot2_3.3.6 sass_0.4.2 biomaRt_2.53.2
[67] rpart_4.1.16 latticeExtra_0.6-30 stringi_1.7.8
[70] RSQLite_2.2.15 highr_0.9 BiocIO_1.7.1
[73] plotrix_3.8-2 checkmate_2.1.0 filelock_1.0.2
[76] BiocParallel_1.31.10 rlang_1.0.4 pkgconfig_2.0.3
[79] bitops_1.0-7 evaluate_0.15 lattice_0.20-45
[82] Rhdf5lib_1.19.2 purrr_0.3.4 GenomicAlignments_1.33.0 [85] htmlwidgets_1.5.4 bit_4.0.4 tidyselect_1.1.2
[88] [au:] magrittr_2.0.3 R6_2.5.1 generics_0.1.3
[91] Hmisc_4.7-0 DelayedArray_0.23.0 DBI_1.1.3
[94] pillar_1.8.0 foreign_0.8-82 survivval_3 .3-1
[97] KEGGREST_1.37.3 RCurl_1.98-1.7 nnet_7.3-17
[100] tibble_3.1.7 crayon_1.5.1 interp_1.1-3
[103] utf8_1.2.2 BiocFileCache_2.5.0 rmarkdown_2.14
[106] jpeg_0.1-9 progress_1.2.2 data.table_1.14.2
[109] Rgraphviz_2.41.1 blob_1.2.3 digest_0.6.29
[112]王晓明