Tutorial for making track plots to visualize finemapping results for genomic regions
Kaixuan Luo
Last updated: 2022-09-12
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| File | Version | Author | Date | Message |
|---|---|---|---|---|
| Rmd | adbc5ca | kevinlkx | 2022-09-12 | added ABC data |
| html | ff411be | kevinlkx | 2022-09-12 | Build site. |
| Rmd | 2b0f109 | kevinlkx | 2022-09-12 | updated trackplot with gtf based txdb |
| html | 76c1546 | kevinlkx | 2022-09-12 | Build site. |
| Rmd | cdf3452 | kevinlkx | 2022-09-12 | added txdb built from gtf |
| html | 45bb194 | kevinlkx | 2022-08-19 | Build site. |
| Rmd | 6e9c89d | kevinlkx | 2022-08-19 | added a note about counts data format |
| html | ca16d13 | kevinlkx | 2022-08-18 | Build site. |
| Rmd | f05e951 | kevinlkx | 2022-08-18 | added a tutorial for making track plots |
| Rmd | 5295f53 | kevinlkx | 2022-08-18 | added trackplot tutorials |
Track plot tutorial
Required input data:
- Genetic fine-mapping summary statistics.
- Gene annotations (exons, introns, UTRs, etc.).
- Functional annotation data, e.g.: ATAC-seq data, histone ChIP-seq peaks, PC-HiC loops, etc.
To make the trackplots, you will need to have the following packages
installed: AnnotationDbi, org.Hs.eg.db,
GenomicInteractions, Gviz,
rtracklayer from Bioconductor.
Load R packages
suppressMessages(library(data.table))
suppressMessages(library(tidyverse))
suppressMessages(library(GenomicRanges))
suppressMessages(library(AnnotationDbi)) # match gene ID to gene symbol
suppressMessages(library(org.Hs.eg.db)) # match gene ID to gene symbol
suppressMessages(library(GenomicInteractions)) # visualize HiC plots
suppressMessages(library(rtracklayer)) # loading bigwigs/bed files
suppressMessages(library(bigsnpr)) # loading genotype data from 1000Genomes for LD calculation
suppressMessages(library(Gviz)) # make track plots
library(mapgen)
source("code/mapgen_trackplots.R")data.dir <- "/project2/xinhe/kevinluo/gene-level-finemapping/trackplot_tutorial/data"Load fine-mapping results.
finemapstats <- readRDS(system.file("extdata", "aFib_Finemapped.tble.rds", package = "mapgen"))
finemapstats.gr <- process_finemapping_sumstats(finemapstats,
snp = 'snp', chr = 'chr',
pos = 'pos', pip = 'susie_pip',
pval = 'pval', zscore = 'zscore',
cs = 'CS', locus = 'locus',
pip.thresh = 0)Processing fine-mapping summary statistics ...Load genomic annotations and gene information
genomic.annots <- readRDS(system.file("extdata", "genomic.annots.hg19.gr.rds", package = "mapgen"))
gene.annots <- genomic.annots$genesLoad Promoter-capture HiC (PCHi-C) data from iPSC derived cardiomyocytes (CMs).
pcHiC.gr <- readRDS(system.file("extdata", "pcHiC.CM.gr.rds", package = "mapgen"))Load ABC data
ABC <- fread(file.path(data.dir, "heart_ventricle-ENCODE_ABC.tsv.gz"))
ABC.gr <- process_ABC(ABC, ABC.thresh = 0.015, full.element = TRUE)
ABC.gr <- ABC.gr[ABC.gr$gene_name %in% gene.annots$gene_name, ] # restrict to protein coding genes
ABC.gr$score <- ABC.gr$ABC.Score * 100Load H3K27ac and DHS bed files
H3K27ac_peaks <- rtracklayer::import(file.path(data.dir, "H3K27ac_heart_concat.bed"))
DHS_peaks <- rtracklayer::import(file.path(data.dir, "FetalHeart_E083-DNase_hg19_cleaned_narrowPeak.bed.gz"))Load ATAC data files. These data need to be in wig, bigWig/bw, bedGraph, or bam format.
atac_data_files <- c(file.path(data.dir, "Hg19_Cardiomyocyte-TileSize-500-normMethod-ReadsInTSS-ArchR.bw.bedGraph"),
file.path(data.dir, "Hg19_Endothelial-TileSize-500-normMethod-ReadsInTSS-ArchR.bw.bedGraph"),
file.path(data.dir, "Hg19_Fibroblast-TileSize-500-normMethod-ReadsInTSS-ArchR.bw.bedGraph"))
atac_data <- lapply(atac_data_files, function(x){rtracklayer::import(x)})
names(atac_data) <- c("Cardiomyocyte", "Endothelial", "Fibroblast")Make a track plot to visualize a locus
Load gene mapping result
gene.mapping.res <- readRDS(file.path(data.dir, "aFib_Finemapped_GeneMapped_ActivePromoter_07242021.gr.rds"))Get the genomic region for gene of interest
gene.of.interest <- "FGF9"
region <- get_gene_region(gene.mapping.res, gene.of.interest, ext = 10000)# Load the txdb object of the gene annotations
txdb <- AnnotationDbi::loadDb("/project2/xinhe/kevinluo/gene-level-finemapping/annot/gene_annotations/gencode.v19.annotation.gtf.sqlite")Loading required package: GenomicFeaturespeaks <- list("H3K27ac" = H3K27ac_peaks, "DHS" = DHS_peaks)
HiC_loops <- list("PC-HiC" = pcHiC.gr, "ABC" = ABC.gr)
finemapping_annot_trackplot(finemapstats.gr,
region,
gene.annots,
genome = "hg19",
genetrack_db = "txdb",
txdb = txdb,
filter_protein_coding_genes = TRUE,
countsdata = atac_data,
data_colors = c("red", "green", "purple"),
data_ylim = c(0,0.8),
peaks = peaks,
HiC_loops = HiC_loops,
highlight_snps = "topSNP",
verbose = TRUE)Making trackplots ...
6857 snps included.
Adding Cardiomyocyte track...
Adding Endothelial track...
Adding Fibroblast track...
Adding H3K27ac track...
Adding DHS track...
Adding PC-HiC track...
Adding ABC track...
Making gene track object using gene annotations in txdb ...'select()' returned 1:1 mapping between keys and columnsHighlight SNPs: rs9506925 
| Version | Author | Date |
|---|---|---|
| 76c1546 | kevinlkx | 2022-09-12 |
sessionInfo()R version 4.2.0 (2022-04-22)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)
Matrix products: default
BLAS/LAPACK: /software/openblas-0.3.13-el7-x86_64/lib/libopenblas_haswellp-r0.3.13.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=C
[4] LC_COLLATE=C LC_MONETARY=C LC_MESSAGES=C
[7] LC_PAPER=C LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=C LC_IDENTIFICATION=C
attached base packages:
[1] grid stats4 stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] GenomicFeatures_1.48.3 mapgen_0.3.10.9000
[3] Gviz_1.40.1 bigsnpr_1.10.8
[5] bigstatsr_1.5.6 rtracklayer_1.56.0
[7] GenomicInteractions_1.30.0 InteractionSet_1.24.0
[9] SummarizedExperiment_1.26.1 MatrixGenerics_1.8.0
[11] matrixStats_0.62.0 org.Hs.eg.db_3.15.0
[13] AnnotationDbi_1.58.0 Biobase_2.56.0
[15] GenomicRanges_1.48.0 GenomeInfoDb_1.32.2
[17] IRanges_2.30.0 S4Vectors_0.34.0
[19] BiocGenerics_0.42.0 forcats_0.5.1
[21] stringr_1.4.0 dplyr_1.0.9
[23] purrr_0.3.4 readr_2.1.2
[25] tidyr_1.2.0 tibble_3.1.7
[27] ggplot2_3.3.6 tidyverse_1.3.1
[29] data.table_1.14.2 workflowr_1.7.0
loaded via a namespace (and not attached):
[1] utf8_1.2.2 R.utils_2.11.0 tidyselect_1.1.2
[4] RSQLite_2.2.14 htmlwidgets_1.5.4 BiocParallel_1.30.3
[7] munsell_0.5.0 codetools_0.2-18 interp_1.1-3
[10] withr_2.5.0 colorspace_2.0-3 filelock_1.0.2
[13] highr_0.9 knitr_1.39 rstudioapi_0.13
[16] git2r_0.30.1 GenomeInfoDbData_1.2.8 bit64_4.0.5
[19] rprojroot_2.0.3 vctrs_0.4.1 generics_0.1.2
[22] xfun_0.30 biovizBase_1.44.0 BiocFileCache_2.4.0
[25] R6_2.5.1 bigassertr_0.1.5 doParallel_1.0.17
[28] bigsparser_0.6.1 AnnotationFilter_1.20.0 bitops_1.0-7
[31] cachem_1.0.6 DelayedArray_0.22.0 assertthat_0.2.1
[34] promises_1.2.0.1 BiocIO_1.6.0 scales_1.2.0
[37] nnet_7.3-17 gtable_0.3.0 processx_3.5.3
[40] ensembldb_2.20.2 rlang_1.0.2 flock_0.7
[43] splines_4.2.0 lazyeval_0.2.2 dichromat_2.0-0.1
[46] broom_0.8.0 checkmate_2.1.0 yaml_2.3.5
[49] bigparallelr_0.3.2 modelr_0.1.8 backports_1.4.1
[52] httpuv_1.6.5 Hmisc_4.7-1 tools_4.2.0
[55] ellipsis_0.3.2 jquerylib_0.1.4 RColorBrewer_1.1-3
[58] Rcpp_1.0.8.3 base64enc_0.1-3 progress_1.2.2
[61] zlibbioc_1.42.0 RCurl_1.98-1.7 ps_1.7.0
[64] prettyunits_1.1.1 rpart_4.1.16 deldir_1.0-6
[67] cowplot_1.1.1 haven_2.5.0 cluster_2.1.3
[70] fs_1.5.2 magrittr_2.0.3 reprex_2.0.1
[73] whisker_0.4 ProtGenerics_1.28.0 hms_1.1.1
[76] evaluate_0.15 XML_3.99-0.9 jpeg_0.1-9
[79] readxl_1.4.0 gridExtra_2.3 compiler_4.2.0
[82] biomaRt_2.52.0 crayon_1.5.1 R.oo_1.24.0
[85] htmltools_0.5.2 later_1.3.0 tzdb_0.3.0
[88] Formula_1.2-4 lubridate_1.8.0 DBI_1.1.3
[91] dbplyr_2.1.1 rappdirs_0.3.3 Matrix_1.4-1
[94] cli_3.3.0 R.methodsS3_1.8.1 parallel_4.2.0
[97] igraph_1.3.4 pkgconfig_2.0.3 getPass_0.2-2
[100] GenomicAlignments_1.32.0 foreign_0.8-82 xml2_1.3.3
[103] foreach_1.5.2 bslib_0.3.1 rngtools_1.5.2
[106] XVector_0.36.0 rvest_1.0.2 doRNG_1.8.2
[109] VariantAnnotation_1.42.1 callr_3.7.0 digest_0.6.29
[112] Biostrings_2.64.0 rmarkdown_2.14 cellranger_1.1.0
[115] htmlTable_2.4.0 restfulr_0.0.14 curl_4.3.2
[118] Rsamtools_2.12.0 rjson_0.2.21 lifecycle_1.0.1
[121] jsonlite_1.8.0 BSgenome_1.64.0 fansi_1.0.3
[124] pillar_1.7.0 lattice_0.20-45 KEGGREST_1.36.2
[127] fastmap_1.1.0 httr_1.4.3 survival_3.3-1
[130] glue_1.6.2 png_0.1-7 iterators_1.0.14
[133] bit_4.0.4 stringi_1.7.6 sass_0.4.1
[136] blob_1.2.3 latticeExtra_0.6-30 memoise_2.0.1