Plotting issues (compartment_matrixplot, ATA plot) #360
Description
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