Open ratheraarif opened 7 months ago
when I execute the following code on my own hic data I do not get the score column and therefore not able to generate the plot
hic
I only get the following columns seqnames, start, end, width, strand ,viewpoint, center, in_viewpoint sample
seqnames, start, end, width, strand ,viewpoint, center, in_viewpoint sample
please my HiC data have chromnames as chr1, chr2,....,chr16
``v4c_centro <- imap(hics, ~ virtual4C(.x, GenomicRanges::resize(centros_yeast[2], 8000)) |> as_tibble() |> mutate(sample = .y) |> filter(seqnames == 'chr4') )
ggplot(v4c_centro, aes(x = start, y = score, fill = sample)) + geom_area() + theme_bw() + labs( x = "chrIV position", y = "Contacts with chrII centromere", title = "Interaction profile of chrII centromere" ) + coord_cartesian(ylim = c(0, 0.015))``
R version 4.3.2 (2023-10-31) Platform: aarch64-apple-darwin20 (64-bit) Running under: macOS Sonoma 14.3 Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.11.0 locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 time zone: Asia/Kolkata tzcode source: internal attached base packages: [1] stats4 stats graphics grDevices utils datasets methods base other attached packages: [1] purrr_1.0.2 diffHic_1.34.0 InteractionSet_1.30.0 [4] SummarizedExperiment_1.32.0 Biobase_2.62.0 MatrixGenerics_1.14.0 [7] matrixStats_1.2.0 GenomicRanges_1.54.1 GenomeInfoDb_1.38.5 [10] IRanges_2.36.0 S4Vectors_0.40.2 dplyr_1.1.4 [13] Cairo_1.6-2 DNAZooData_1.2.0 fourDNData_1.2.0 [16] HiContactsData_1.4.0 ExperimentHub_2.10.0 AnnotationHub_3.10.0 [19] BiocFileCache_2.10.1 dbplyr_2.4.0 BiocGenerics_0.48.1 [22] HiCool_1.2.0 ggplot2_3.4.4 HiContacts_1.4.0 [25] HiCExperiment_1.3.1 loaded via a namespace (and not attached): [1] strawr_0.0.91 rstudioapi_0.15.0 [3] jsonlite_1.8.8 magrittr_2.0.3 [5] ggbeeswarm_0.7.2 farver_2.1.1 [7] rmarkdown_2.25 BiocIO_1.12.0 [9] zlibbioc_1.48.0 vctrs_0.6.5 [11] memoise_2.0.1 Rsamtools_2.18.0 [13] RCurl_1.98-1.14 htmltools_0.5.7 [15] S4Arrays_1.2.0 curl_5.2.0 [17] Rhdf5lib_1.24.1 SparseArray_1.2.3 [19] rhdf5_2.46.1 htmlwidgets_1.6.4 [21] basilisk_1.14.2 plotly_4.10.4 [23] cachem_1.0.8 GenomicAlignments_1.38.2 [25] mime_0.12 lifecycle_1.0.4 [27] pkgconfig_2.0.3 Matrix_1.6-5 [29] R6_2.5.1 fastmap_1.1.1 [31] GenomeInfoDbData_1.2.11 shiny_1.8.0 [33] digest_0.6.34 colorspace_2.1-0 [35] AnnotationDbi_1.64.1 plyinteractions_1.1.0 [37] RSpectra_0.16-1 pkgload_1.3.4 [39] RSQLite_2.3.5 Rhtslib_2.4.1 [41] labeling_0.4.3 filelock_1.0.3 [43] fansi_1.0.6 httr_1.4.7 [45] abind_1.4-5 compiler_4.3.2 [47] bit64_4.0.5 withr_3.0.0 [49] csaw_1.36.1 BiocParallel_1.36.0 [51] DBI_1.2.0 highr_0.10 [53] rappdirs_0.3.3 DelayedArray_0.28.0 [55] sessioninfo_1.2.2 rjson_0.2.21 [57] tools_4.3.2 vipor_0.4.7 [59] beeswarm_0.4.0 interactiveDisplayBase_1.40.0 [61] httpuv_1.6.14 glue_1.7.0 [63] restfulr_0.0.15 promises_1.2.1 [65] rhdf5filters_1.14.1 grid_4.3.2 [67] generics_0.1.3 BSgenome_1.70.1 [69] gtable_0.3.4 tzdb_0.4.0 [71] rmdformats_1.0.4 tidyr_1.3.1 [73] data.table_1.14.10 hms_1.1.3 [75] metapod_1.10.1 utf8_1.2.4 [77] XVector_0.42.0 BiocVersion_3.18.1 [79] pillar_1.9.0 stringr_1.5.1 [81] limma_3.58.1 vroom_1.6.5 [83] later_1.3.2 lattice_0.22-5 [85] rtracklayer_1.62.0 bit_4.0.5 [87] tidyselect_1.2.0 locfit_1.5-9.8 [89] Biostrings_2.70.1 knitr_1.45 [91] bookdown_0.37 edgeR_4.0.12 [93] xfun_0.41 statmod_1.5.0 [95] stringi_1.8.3 lazyeval_0.2.2 [97] yaml_2.3.8 evaluate_0.23 [99] codetools_0.2-19 tibble_3.2.1 [101] BiocManager_1.30.22 cli_3.6.2 [103] xtable_1.8-4 reticulate_1.34.0 [105] munsell_0.5.0 Rcpp_1.0.12 [107] dir.expiry_1.10.0 png_0.1-8 [109] XML_3.99-0.16.1 ggrastr_1.0.2 [111] parallel_4.3.2 ellipsis_0.3.2 [113] readr_2.1.5 blob_1.2.4 [115] basilisk.utils_1.14.1 plyranges_1.22.0 [117] bitops_1.0-7 viridisLite_0.4.2 [119] scales_1.3.0 crayon_1.5.2 [121] rlang_1.1.3 KEGGREST_1.42.0 [123] cowplot_1.1.3
Are the maps stored in hics overlapping with centros_yeast[2]? If your input map does not overlap with the targeted viewpoint, no scores will be computed.
hics
centros_yeast[2]
scores
when I execute the following code on my own
hic
data I do not get the score column and therefore not able to generate the plotI only get the following columns
seqnames, start, end, width, strand ,viewpoint, center, in_viewpoint sample
please my HiC data have chromnames as chr1, chr2,....,chr16
``v4c_centro <- imap(hics, ~ virtual4C(.x, GenomicRanges::resize(centros_yeast[2], 8000)) |> as_tibble() |> mutate(sample = .y) |> filter(seqnames == 'chr4') )
ggplot(v4c_centro, aes(x = start, y = score, fill = sample)) + geom_area() + theme_bw() + labs( x = "chrIV position", y = "Contacts with chrII centromere", title = "Interaction profile of chrII centromere" ) + coord_cartesian(ylim = c(0, 0.015))``