score column not generated
ratheraarif opened this issue · comments
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
I 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))``
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.