Open tinyimp80 opened 1 month ago
Thank you for developing such a great tool. I got some plotting error.
> CS_out <- compartment_score(list(Control_100kb,Treat_100kb), bed = H3K27acPeaks) > compartment_matrixplot( exp1 = Control_100kb, exp2 = Treat_100kb, CS_discovery = CS_out, chrom = "chrX", arm = "q", colour_lim = c(0, 15) )
The compartment track on the Y axis is upside down.
And in the ATA plot, the positions of individual and difference have been switched.
> Treat_10kb_list <- list("Control" = Control_10kb, "Treat" = Treat_10kb) > ATA_Treat_COcalls <- ATA(Treat_10kb_list, bed = TAD_Co) > visualise(ATA_Treat_COcalls, colour_lim = c(0,50), colour_lim_contrast = c(-5,5), metric = 'diff', focus = 1)
Plz, help me resolve the issue.
> sessionInfo() R version 4.3.3 (2024-02-29) Platform: x86_64-conda-linux-gnu (64-bit) Running under: Ubuntu 16.04.7 LTS Matrix products: default BLAS/LAPACK: /home/tinyimp/miniconda3/envs/R/lib/libopenblasp-r0.3.27.so; LAPACK version 3.12.0 locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=ko_KR.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=ko_KR.UTF-8 [6] LC_MESSAGES=en_US.UTF-8 LC_PAPER=ko_KR.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=ko_KR.UTF-8 LC_IDENTIFICATION=C time zone: Asia/Seoul tzcode source: system (glibc) attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] ggplot2_3.5.1 GENOVA_1.0.1 loaded via a namespace (and not attached): [1] vctrs_0.6.5 cli_3.6.2 rlang_1.1.3 purrr_1.0.2 generics_0.1.3 textshaping_0.4.0 data.table_1.15.4 [8] glue_1.7.0 labeling_0.4.3 colorspace_2.1-0 ragg_1.3.2 scales_1.3.0 fansi_1.0.6 grid_4.3.3 [15] munsell_0.5.1 tibble_3.2.1 yaml_2.3.8 lifecycle_1.0.4 compiler_4.3.3 dplyr_1.1.4 pkgconfig_2.0.3 [22] tidyr_1.3.1 rstudioapi_0.16.0 systemfonts_1.1.0 farver_2.1.2 R6_2.5.1 tidyselect_1.2.1 utf8_1.2.4 [29] pillar_1.9.0 magrittr_2.0.3 tools_4.3.3 withr_3.0.0 gtable_0.3.5 R version 4.3.3 (2024-02-29) Platform: x86_64-conda-linux-gnu (64-bit) Running under: Ubuntu 16.04.7 LTS Matrix products: default BLAS/LAPACK: /home/tinyimp/miniconda3/envs/R/lib/libopenblasp-r0.3.27.so; LAPACK version 3.12.0 locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=ko_KR.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=ko_KR.UTF-8 [6] LC_MESSAGES=en_US.UTF-8 LC_PAPER=ko_KR.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=ko_KR.UTF-8 LC_IDENTIFICATION=C time zone: Asia/Seoul tzcode source: system (glibc) attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] ggplot2_3.5.1 GENOVA_1.0.1 loaded via a namespace (and not attached): [1] vctrs_0.6.5 cli_3.6.2 rlang_1.1.3 purrr_1.0.2 generics_0.1.3 textshaping_0.4.0 data.table_1.15.4 [8] glue_1.7.0 labeling_0.4.3 colorspace_2.1-0 ragg_1.3.2 scales_1.3.0 fansi_1.0.6 grid_4.3.3 [15] munsell_0.5.1 tibble_3.2.1 yaml_2.3.8 lifecycle_1.0.4 compiler_4.3.3 dplyr_1.1.4 pkgconfig_2.0.3 [22] tidyr_1.3.1 rstudioapi_0.16.0 systemfonts_1.1.0 farver_2.1.2 R6_2.5.1 tidyselect_1.2.1 utf8_1.2.4 [29] pillar_1.9.0 magrittr_2.0.3 tools_4.3.3 withr_3.0.0 gtable_0.3.5
Thank you for developing such a great tool. I got some plotting error.
And in the ATA plot, the positions of individual and difference have been switched.
Plz, help me resolve the issue.