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GreenleafLab / ArchR

ArchR : Analysis of Regulatory Chromatin in R (www.ArchRProject.com)
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Black mask in plotEnrichHeatmap when `transpose = F` #1780

Closed Zepeng-Mu closed 1 year ago

Zepeng-Mu commented 1 year ago

Hello,

I'm using the dev branch of ArchR, and found that plotEnrichHeatmap generates a black heatmap when transpose = F. Screenshot 2022-12-20 at 13 42 57 Screenshot 2022-12-20 at 13 42 46

If you look at the bottom one really hard, you kind of see the heatmap beneath the very black mask above it. I do not recall having this issue before with previous versions of ArchR.

Here is the session info:

> session_info()
─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
 setting  value
 version  R version 4.2.0 (2022-04-22)
 os       Ubuntu 20.04.4 LTS
 system   x86_64, linux-gnu
 ui       RStudio
 language (EN)
 collate  en_US.UTF-8
 ctype    en_US.UTF-8
 tz       Etc/UTC
 date     2022-12-20
 rstudio  2022.02.3+492 Prairie Trillium (server)
 pandoc   2.14.2 @ /scratch/midway3/zepengmu/miniconda3/bin/pandoc

─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
 package              * version    date (UTC) lib source
 AnnotationDbi        * 1.58.0     2022-04-26 [1] Bioconductor
 ape                    5.6-2      2022-03-02 [1] CRAN (R 4.2.0)
 aplot                  0.1.7      2022-09-06 [1] CRAN (R 4.2.0)
 ArchR                * 1.0.3      2022-12-05 [1] Github (GreenleafLab/ArchR@3f87fb6)
 ashr                   2.2-57     2022-12-12 [1] Github (stephens999/ashr@4cad5c4)
 assertthat             0.2.1      2019-03-21 [1] CRAN (R 4.2.0)
 backports              1.4.1      2021-12-13 [1] CRAN (R 4.2.0)
 beachmat               2.12.0     2022-04-26 [1] Bioconductor
 beeswarm               0.4.0      2021-06-01 [1] CRAN (R 4.2.0)
 Biobase              * 2.56.0     2022-04-26 [1] Bioconductor
 BiocGenerics         * 0.42.0     2022-04-26 [1] Bioconductor
 BiocParallel           1.30.4     2022-10-11 [1] Bioconductor
 Biostrings             2.64.1     2022-08-18 [1] Bioconductor
 bit                    4.0.5      2022-11-15 [1] CRAN (R 4.2.0)
 bit64                  4.0.5      2020-08-30 [1] CRAN (R 4.2.0)
 bitops                 1.0-7      2021-04-24 [1] CRAN (R 4.2.0)
 blob                   1.2.3      2022-04-10 [1] CRAN (R 4.2.0)
 boot                   1.3-28     2021-05-03 [1] CRAN (R 4.2.1)
 broom                * 1.0.1      2022-08-29 [1] CRAN (R 4.2.0)
 cachem                 1.0.6      2021-08-19 [1] CRAN (R 4.2.0)
 Cairo                  1.5-15     2022-03-16 [1] CRAN (R 4.2.0)
 callr                  3.7.3      2022-11-02 [1] CRAN (R 4.2.0)
 cellranger             1.1.0      2016-07-27 [1] CRAN (R 4.2.0)
 circlize             * 0.4.15     2022-05-10 [1] CRAN (R 4.2.0)
 cli                    3.4.1      2022-09-23 [1] CRAN (R 4.2.0)
 clue                   0.3-63     2022-11-19 [1] CRAN (R 4.2.0)
 cluster                2.1.4      2022-08-22 [1] CRAN (R 4.2.0)
 clusterProfiler      * 4.4.4      2022-06-21 [1] Bioconductor
 coda                   0.19-4     2020-09-30 [1] CRAN (R 4.2.0)
 codetools              0.2-18     2020-11-04 [1] CRAN (R 4.2.0)
 colorspace             2.0-3      2022-02-21 [1] CRAN (R 4.2.0)
 ComplexHeatmap       * 2.12.1     2022-08-09 [1] Bioconductor
 cowplot              * 1.1.1      2020-12-30 [1] CRAN (R 4.2.0)
 crayon                 1.5.2      2022-09-29 [1] CRAN (R 4.2.0)
 data.table           * 1.14.6     2022-11-16 [1] CRAN (R 4.2.0)
 DBI                    1.1.3      2022-06-18 [1] CRAN (R 4.2.0)
 dbplyr                 2.1.1      2021-04-06 [1] CRAN (R 4.2.0)
 DelayedArray           0.22.0     2022-04-26 [1] Bioconductor
 DelayedMatrixStats     1.18.2     2022-10-13 [1] Bioconductor
 devtools             * 2.4.5      2022-10-11 [1] CRAN (R 4.2.0)
 digest                 0.6.31     2022-12-11 [1] CRAN (R 4.2.0)
 distances              0.1.8.9000 2022-12-20 [1] Github (fsavje/distances@884bfb9)
 DO.db                  2.9        2022-10-08 [1] Bioconductor
 doParallel             1.0.17     2022-02-07 [1] CRAN (R 4.2.0)
 DOSE                   3.22.1     2022-08-30 [1] Bioconductor
 downloader             0.4        2015-07-09 [1] CRAN (R 4.2.0)
 dplyr                * 1.0.10     2022-09-01 [1] CRAN (R 4.2.0)
 ellipsis               0.3.2      2021-04-29 [1] CRAN (R 4.2.0)
 enrichplot             1.16.2     2022-08-30 [1] Bioconductor
 fansi                  1.0.3      2022-03-24 [1] CRAN (R 4.2.0)
 farver                 2.1.1      2022-07-06 [1] CRAN (R 4.2.0)
 fastmap                1.1.0      2021-01-25 [1] CRAN (R 4.2.0)
 fastmatch              1.1-3      2021-07-23 [1] CRAN (R 4.2.0)
 fastTopics           * 0.6-142    2022-11-30 [1] Github (stephenslab/fastTopics@d53a14a)
 fgsea                  1.22.0     2022-04-26 [1] Bioconductor
 forcats              * 0.5.2      2022-08-19 [1] CRAN (R 4.2.0)
 foreach                1.5.2      2022-02-02 [1] CRAN (R 4.2.0)
 fs                     1.5.2      2021-12-08 [1] CRAN (R 4.2.0)
 generics               0.1.3      2022-07-05 [1] CRAN (R 4.2.0)
 GenomeInfoDb         * 1.34.4     2022-12-01 [1] Bioconductor
 GenomeInfoDbData       1.2.8      2022-09-10 [1] Bioconductor
 GenomicRanges        * 1.48.0     2022-04-26 [1] Bioconductor
 GetoptLong             1.0.5      2020-12-15 [1] CRAN (R 4.2.0)
 ggbeeswarm             0.6.0      2017-08-07 [1] CRAN (R 4.2.0)
 ggforce                0.4.1      2022-10-04 [1] CRAN (R 4.2.0)
 ggfun                  0.0.7      2022-08-31 [1] CRAN (R 4.2.0)
 ggplot2              * 3.4.0      2022-11-04 [1] CRAN (R 4.2.0)
 ggplotify              0.1.0      2021-09-02 [1] CRAN (R 4.2.0)
 ggprism                1.0.3      2021-06-08 [1] CRAN (R 4.2.0)
 ggraph                 2.0.6      2022-08-08 [1] CRAN (R 4.2.0)
 ggrastr                1.0.1      2021-12-08 [1] CRAN (R 4.2.0)
 ggrepel              * 0.9.2.9999 2022-12-12 [1] Github (slowkow/ggrepel@e9bcb75)
 ggtext                 0.1.2      2022-09-16 [1] CRAN (R 4.2.0)
 ggtree                 3.4.4      2022-09-27 [1] Bioconductor
 GlobalOptions          0.1.2      2020-06-10 [1] CRAN (R 4.2.0)
 glue                   1.6.2      2022-02-24 [1] CRAN (R 4.2.0)
 GO.db                  3.15.0     2022-09-10 [1] Bioconductor
 GOSemSim               2.22.0     2022-04-26 [1] Bioconductor
 graphlayouts           0.8.2      2022-09-29 [1] CRAN (R 4.2.0)
 gridExtra            * 2.3        2017-09-09 [1] CRAN (R 4.2.0)
 gridGraphics           0.5-1      2020-12-13 [1] CRAN (R 4.2.0)
 gridtext               0.1.5      2022-09-16 [1] CRAN (R 4.2.0)
 gtable               * 0.3.1      2022-09-01 [1] CRAN (R 4.2.0)
 gtools               * 3.9.4      2022-11-27 [1] CRAN (R 4.2.0)
 haven                  2.5.0      2022-04-15 [1] CRAN (R 4.2.0)
 hms                    1.1.2      2022-08-19 [1] CRAN (R 4.2.0)
 htmltools              0.5.3      2022-07-18 [1] CRAN (R 4.2.0)
 htmlwidgets            1.5.4      2021-09-08 [1] CRAN (R 4.2.0)
 httpuv                 1.6.6      2022-09-08 [1] CRAN (R 4.2.0)
 httr                   1.4.4      2022-08-17 [1] CRAN (R 4.2.0)
 igraph                 1.3.4      2022-07-19 [1] CRAN (R 4.2.0)
 invgamma               1.1        2017-05-07 [1] CRAN (R 4.2.0)
 IRanges              * 2.30.1     2022-08-18 [1] Bioconductor
 irlba                  2.3.5.1    2022-10-03 [1] CRAN (R 4.2.0)
 iterators              1.0.14     2022-02-05 [1] CRAN (R 4.2.1)
 jsonlite               1.8.4      2022-12-06 [1] CRAN (R 4.2.0)
 KEGGREST               1.36.3     2022-07-12 [1] Bioconductor
 labeling               0.4.2      2020-10-20 [1] CRAN (R 4.2.0)
 later                  1.3.0      2021-08-18 [1] CRAN (R 4.2.0)
 lattice                0.20-45    2021-09-22 [1] CRAN (R 4.2.0)
 lazyeval               0.2.2      2019-03-15 [1] CRAN (R 4.2.0)
 lifecycle              1.0.3      2022-10-07 [1] CRAN (R 4.2.0)
 lme4                 * 1.1-32     2022-12-12 [1] Github (lme4/lme4@aab627f)
 lubridate              1.8.0      2021-10-07 [1] CRAN (R 4.2.0)
 magrittr             * 2.0.3      2022-03-30 [1] CRAN (R 4.2.0)
 markdown               1.1        2019-08-07 [1] CRAN (R 4.2.0)
 MASS                   7.3-58.1   2022-08-03 [1] CRAN (R 4.2.0)
 Matrix               * 1.5-3      2022-11-11 [1] CRAN (R 4.2.0)
 MatrixGenerics       * 1.8.1      2022-06-26 [1] Bioconductor
 MatrixModels           0.5-1      2022-09-11 [1] CRAN (R 4.2.0)
 matrixStats          * 0.63.0     2022-11-18 [1] CRAN (R 4.2.0)
 mcmc                   0.9-7      2020-03-21 [1] CRAN (R 4.2.0)
 MCMCpack               1.6-3      2022-04-13 [1] CRAN (R 4.2.0)
 memoise                2.0.1      2021-11-26 [1] CRAN (R 4.2.0)
 mime                   0.12       2021-09-28 [1] CRAN (R 4.2.0)
 miniUI                 0.1.1.1    2018-05-18 [1] CRAN (R 4.2.0)
 minqa                  1.2.5      2022-10-19 [1] CRAN (R 4.2.0)
 mixsqp                 0.3-48     2022-11-16 [1] CRAN (R 4.2.0)
 modelr                 0.1.8      2020-05-19 [1] CRAN (R 4.2.0)
 munsell                0.5.0      2018-06-12 [1] CRAN (R 4.2.0)
 nlme                   3.1-160    2022-10-10 [1] CRAN (R 4.2.0)
 nloptr                 2.0.3      2022-05-26 [1] CRAN (R 4.2.0)
 org.Hs.eg.db         * 3.15.0     2022-11-20 [1] Bioconductor
 patchwork              1.1.2      2022-08-19 [1] CRAN (R 4.2.0)
 pbapply                1.5-0      2021-09-16 [1] CRAN (R 4.2.0)
 Phoenix              * 0.0.0.9000 2022-09-19 [1] local
 pillar                 1.8.1      2022-08-19 [1] CRAN (R 4.2.0)
 pkgbuild               1.4.0      2022-11-27 [1] CRAN (R 4.2.0)
 pkgconfig              2.0.3      2019-09-22 [1] CRAN (R 4.2.0)
 pkgload                1.3.2      2022-11-16 [1] CRAN (R 4.2.0)
 plotly                 4.10.1     2022-11-07 [1] CRAN (R 4.2.0)
 plyr                 * 1.8.8      2022-11-11 [1] CRAN (R 4.2.0)
 png                    0.1-8      2022-11-29 [1] CRAN (R 4.2.0)
 polyclip               1.10-0     2019-03-14 [1] CRAN (R 4.2.0)
 prettyunits            1.1.1      2020-01-24 [1] CRAN (R 4.2.0)
 processx               3.8.0      2022-10-26 [1] CRAN (R 4.2.0)
 profvis                0.3.7      2020-11-02 [1] CRAN (R 4.2.0)
 progress               1.2.2      2019-05-16 [1] CRAN (R 4.2.0)
 promises               1.2.0.1    2021-02-11 [1] CRAN (R 4.2.0)
 ps                     1.7.2      2022-10-26 [1] CRAN (R 4.2.0)
 purrr                * 0.3.5      2022-10-06 [1] CRAN (R 4.2.0)
 quadprog               1.5-8      2019-11-20 [1] CRAN (R 4.2.0)
 quantreg               5.94       2022-07-20 [1] CRAN (R 4.2.0)
 qvalue                 2.28.0     2022-04-26 [1] Bioconductor
 R6                     2.5.1      2021-08-19 [1] CRAN (R 4.2.0)
 ragg                   1.2.2      2022-02-21 [1] CRAN (R 4.2.0)
 RColorBrewer         * 1.1-3      2022-04-03 [1] CRAN (R 4.2.0)
 Rcpp                 * 1.0.9      2022-07-08 [1] CRAN (R 4.2.0)
 RcppArmadillo        * 0.11.4.2.1 2022-11-09 [1] CRAN (R 4.2.0)
 RcppParallel           5.1.5      2022-01-05 [1] CRAN (R 4.2.0)
 RCurl                  1.98-1.9   2022-10-03 [1] CRAN (R 4.2.0)
 readr                * 2.1.3      2022-10-01 [1] CRAN (R 4.2.0)
 readxl                 1.4.0      2022-03-28 [1] CRAN (R 4.2.0)
 remotes                2.4.2      2021-11-30 [1] CRAN (R 4.2.0)
 reprex                 2.0.1      2021-08-05 [1] CRAN (R 4.2.0)
 reshape2               1.4.4      2020-04-09 [1] CRAN (R 4.2.0)
 rhdf5                * 2.40.0     2022-04-26 [1] Bioconductor
 rhdf5filters           1.8.0      2022-04-26 [1] Bioconductor
 Rhdf5lib               1.18.2     2022-05-15 [1] Bioconductor
 rjson                  0.2.21     2022-01-09 [1] CRAN (R 4.2.0)
 rlang                  1.0.6      2022-09-24 [1] CRAN (R 4.2.0)
 RSQLite                2.2.19     2022-11-24 [1] CRAN (R 4.2.0)
 rstudioapi             0.14       2022-08-22 [1] CRAN (R 4.2.0)
 Rtsne                  0.16       2022-04-17 [1] CRAN (R 4.2.0)
 rvest                  1.0.2      2021-10-16 [1] CRAN (R 4.2.0)
 S4Vectors            * 0.34.0     2022-04-26 [1] Bioconductor
 scales                 1.2.1      2022-08-20 [1] CRAN (R 4.2.0)
 scatterpie             0.1.8      2022-09-03 [1] CRAN (R 4.2.0)
 scuttle                1.6.3      2022-08-23 [1] Bioconductor
 sessioninfo            1.2.2      2021-12-06 [1] CRAN (R 4.2.0)
 shadowtext             0.1.2      2022-04-22 [1] CRAN (R 4.2.0)
 shape                  1.4.6      2021-05-19 [1] CRAN (R 4.2.0)
 shiny                  1.7.3      2022-10-25 [1] CRAN (R 4.2.0)
 SingleCellExperiment   1.18.1     2022-10-02 [1] Bioconductor
 SparseM                1.81       2021-02-18 [1] CRAN (R 4.2.0)
 sparseMatrixStats    * 1.8.0      2022-04-26 [1] Bioconductor
 SQUAREM                2021.1     2021-01-13 [1] CRAN (R 4.2.0)
 stringi                1.7.8      2022-07-11 [1] CRAN (R 4.2.0)
 stringr              * 1.5.0      2022-12-02 [1] CRAN (R 4.2.0)
 SummarizedExperiment * 1.26.1     2022-04-29 [1] Bioconductor
 survival               3.4-0      2022-08-09 [1] CRAN (R 4.2.0)
 systemfonts            1.0.4      2022-02-11 [1] CRAN (R 4.2.0)
 textshaping            0.3.6      2021-10-13 [1] CRAN (R 4.2.0)
 tibble               * 3.1.8      2022-07-22 [1] CRAN (R 4.2.0)
 tidygraph              1.2.2      2022-08-22 [1] CRAN (R 4.2.0)
 tidyr                * 1.2.1.9001 2022-12-12 [1] Github (tidyverse/tidyr@21818c6)
 tidyselect             1.2.0      2022-10-10 [1] CRAN (R 4.2.0)
 tidytree               0.4.1      2022-09-26 [1] CRAN (R 4.2.0)
 tidyverse            * 1.3.1      2021-04-15 [1] CRAN (R 4.2.0)
 treeio                 1.20.2     2022-08-14 [1] Bioconductor
 truncnorm              1.0-8      2018-02-27 [1] CRAN (R 4.2.0)
 tweenr                 2.0.2      2022-09-06 [1] CRAN (R 4.2.0)
 tzdb                   0.3.0      2022-03-28 [1] CRAN (R 4.2.0)
 urlchecker             1.0.1      2021-11-30 [1] CRAN (R 4.2.0)
 usethis              * 2.1.6      2022-05-25 [1] CRAN (R 4.2.0)
 utf8                   1.2.2      2021-07-24 [1] CRAN (R 4.2.0)
 uwot                   0.1.14     2022-08-22 [1] CRAN (R 4.2.0)
 vctrs                  0.5.1      2022-11-16 [1] CRAN (R 4.2.0)
 vipor                  0.4.5      2017-03-22 [1] CRAN (R 4.2.0)
 viridis                0.6.2      2021-10-13 [1] CRAN (R 4.2.0)
 viridisLite            0.4.1      2022-08-22 [1] CRAN (R 4.2.0)
 withr                  2.5.0      2022-03-03 [1] CRAN (R 4.2.0)
 xml2                   1.3.3      2021-11-30 [1] CRAN (R 4.2.0)
 xtable                 1.8-4      2019-04-21 [1] CRAN (R 4.2.0)
 XVector                0.36.0     2022-04-26 [1] Bioconductor
 yulab.utils            0.0.5      2022-06-30 [1] CRAN (R 4.2.0)
 zlibbioc               1.42.0     2022-04-26 [1] Bioconductor
rcorces commented 1 year ago

Hi @Zepeng-Mu! Thanks for using ArchR! Please make sure that your post belongs in the Issues section. Only bugs and error reports belong in the Issues section. Usage questions and feature requests should be posted in the Discussions section, not in Issues.
Before we help you, you must respond to the following questions unless your original post already contained this information: 1. If you've encountered an error, have you already searched previous Issues to make sure that this hasn't already been solved? 2. Can you recapitulate your error using the tutorial code and dataset? If so, provide a reproducible example. 3. Did you post your log file? If not, add it now. 4. Remove any screenshots that contain text and instead copy and paste the text using markdown's codeblock syntax (three consecutive backticks). You can do this by editing your original post.

rcorces commented 1 year ago

can you downgrade ggplot2 and retry

devtools::install_version("ggplot2", version = "3.3.6", repos = "http://cran.us.r-project.org")
Zepeng-Mu commented 1 year ago

Hi, unloading ggplot2 does not seem to have an effect. I thought plotEnrichHeatmap uses ComplexHeatmap?

rcorces commented 1 year ago

Yes that is true.

I'm not able to recapitulate this error with the tutorial data:

> heatmapEM <- plotEnrichHeatmap(enrichMotifs, n = 7, transpose = TRUE)
ArchR logging to : ArchRLogs/ArchR-plotEnrichHeatmap-2f9ea33e65cfaa-Date-2022-12-21_Time-09-49-41.log
If there is an issue, please report to github with logFile!
Adding Annotations..
Preparing Main Heatmap..
'magick' package is suggested to install to give better rasterization.

Set `ht_opt$message = FALSE` to turn off this message.
> ComplexHeatmap::draw(heatmapEM, heatmap_legend_side = "bot", annotation_legend_side = "bot")
It seems you are using RStudio IDE. `anno_mark()` needs to work with the physical size of the graphics device. It only
generates correct plot in the figure panel, while in the zoomed plot (by clicking the icon 'Zoom') or in the exported plot (by
clicking the icon 'Export'), the connection to heatmap rows/columns might be wrong. You can directly use e.g. pdf() to save
the plot into a file.

Use `ht_opt$message = FALSE` to turn off this message.

image

transpose = FALSE

> heatmapEM <- plotEnrichHeatmap(enrichMotifs, n = 7, transpose = FALSE)
ArchR logging to : ArchRLogs/ArchR-plotEnrichHeatmap-2f9ea33f44227c-Date-2022-12-21_Time-09-49-57.log
If there is an issue, please report to github with logFile!
Preparing Main Heatmap..
'magick' package is suggested to install to give better rasterization.

Set `ht_opt$message = FALSE` to turn off this message.
> ComplexHeatmap::draw(heatmapEM, heatmap_legend_side = "bot", annotation_legend_side = "bot")
It seems you are using RStudio IDE. `anno_mark()` needs to work with the physical size of the graphics device. It only
generates correct plot in the figure panel, while in the zoomed plot (by clicking the icon 'Zoom') or in the exported plot (by
clicking the icon 'Export'), the connection to heatmap rows/columns might be wrong. You can directly use e.g. pdf() to save
the plot into a file.

Use `ht_opt$message = FALSE` to turn off this message.

image

Must be some package incompatibility issue. It looks like you are on a more recent version of ComplexHeatmap and also probably a more recent version of Bioconductor. The most recent Bioconductor release (3.16)has been causing problems with ArchR

Incase it is helpful, here is my sessionInfo()

> session_info()
─ Session info  ────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
 hash: clutch bag, baby bottle, Tokyo tower

 setting  value
 version  R version 4.1.1 (2021-08-10)
 os       Rocky Linux 8.5 (Green Obsidian)
 system   x86_64, linux-gnu
 ui       RStudio
 language (EN)
 collate  en_US.UTF-8
 ctype    en_US.UTF-8
 tz       America/Los_Angeles
 date     2022-12-21
 rstudio  2021.09.2+382 Ghost Orchid (server)
 pandoc   2.14.0.3 @ /usr/lib/rstudio-server/bin/pandoc/ (via rmarkdown)

─ Packages ─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
 ! package                     * version    date (UTC) lib source
 P abind                         1.4-5      2016-07-21 [?] CRAN (R 4.1.1)
 P annotate                      1.72.0     2021-10-26 [?] Bioconductor
 P AnnotationDbi                 1.56.2     2021-11-09 [?] Bioconductor
 P ArchR                       * 1.0.3      2022-12-17 [?] Github (GreenleafLab/ArchR@b243653)
   assertthat                    0.2.1      2019-03-21 [1] CRAN (R 4.1.1)
   beeswarm                      0.4.0      2021-06-01 [1] CRAN (R 4.1.1)
 P Biobase                     * 2.54.0     2021-10-26 [?] Bioconductor
 P BiocGenerics                * 0.40.0     2021-10-26 [?] Bioconductor
 P BiocIO                        1.4.0      2021-10-26 [?] Bioconductor
 P BiocManager                   1.30.16    2021-06-15 [?] CRAN (R 4.1.1)
 P BiocParallel                  1.28.2     2021-11-25 [?] Bioconductor
 P Biostrings                  * 2.62.0     2021-10-26 [?] Bioconductor
 P bit                           4.0.4      2020-08-04 [?] CRAN (R 4.1.1)
 P bit64                         4.0.5      2020-08-30 [?] CRAN (R 4.1.1)
 P bitops                        1.0-7      2021-04-24 [?] CRAN (R 4.1.1)
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 P BSgenome.Hsapiens.UCSC.hg19 * 1.4.3      2021-12-05 [?] Bioconductor
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 P callr                         3.7.0      2021-04-20 [?] CRAN (R 4.1.1)
 P caTools                       1.18.2     2021-03-28 [?] CRAN (R 4.1.1)
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 P fansi                         0.5.0      2021-05-25 [?] CRAN (R 4.1.1)
 P fastmap                       1.1.0      2021-01-25 [?] CRAN (R 4.1.1)
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 P foreach                       1.5.1      2020-10-15 [?] CRAN (R 4.1.1)
 P fs                            1.5.0      2020-07-31 [?] CRAN (R 4.1.1)
   future                        1.29.0     2022-11-06 [1] CRAN (R 4.1.1)
 P future.apply                  1.8.1      2021-08-10 [?] CRAN (R 4.1.1)
 P generics                      0.1.1      2021-10-25 [?] CRAN (R 4.1.1)
 P GenomeInfoDb                * 1.30.0     2021-10-26 [?] Bioconductor
 P GenomeInfoDbData              1.2.7      2021-12-04 [?] Bioconductor
 P GenomicAlignments             1.30.0     2021-10-26 [?] Bioconductor
 P GenomicRanges               * 1.46.1     2021-11-18 [?] Bioconductor
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   ggbeeswarm                    0.6.0      2017-08-07 [1] CRAN (R 4.1.1)
 P ggplot2                     * 3.3.5      2021-06-25 [?] CRAN (R 4.1.1)
   ggrastr                       1.0.1      2021-12-08 [1] CRAN (R 4.1.1)
 P ggrepel                       0.9.1      2021-01-15 [?] CRAN (R 4.1.1)
 P ggridges                      0.5.3      2021-01-08 [?] CRAN (R 4.1.1)
 P GlobalOptions                 0.1.2      2020-06-10 [?] CRAN (R 4.1.1)
   globals                       0.16.2     2022-11-21 [1] CRAN (R 4.1.1)
 P glue                          1.5.1      2021-11-30 [?] CRAN (R 4.1.1)
 P GO.db                         3.14.0     2021-12-04 [?] Bioconductor
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 P gridExtra                   * 2.3        2017-09-09 [?] CRAN (R 4.1.1)
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 P hms                           1.1.1      2021-09-26 [?] CRAN (R 4.1.1)
 P htmltools                     0.5.2      2021-08-25 [?] CRAN (R 4.1.1)
 P htmlwidgets                   1.5.4      2021-09-08 [?] CRAN (R 4.1.1)
 P httpuv                        1.6.3      2021-09-09 [?] CRAN (R 4.1.1)
 P httr                          1.4.2      2020-07-20 [?] CRAN (R 4.1.1)
 P ica                           1.0-2      2018-05-24 [?] CRAN (R 4.1.1)
 P igraph                        1.3.5      2022-09-22 [?] CRAN (R 4.1.1)
 P IRanges                     * 2.28.0     2021-10-26 [?] Bioconductor
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 P iterators                     1.0.13     2020-10-15 [?] CRAN (R 4.1.1)
 P jquerylib                     0.1.4      2021-04-26 [?] CRAN (R 4.1.1)
 P jsonlite                      1.7.2      2020-12-09 [?] CRAN (R 4.1.1)
 P KEGGREST                      1.34.0     2021-10-26 [?] Bioconductor
 P KernSmooth                    2.23-20    2021-05-03 [?] CRAN (R 4.1.1)
 P knitr                         1.41       2022-11-18 [?] CRAN (R 4.1.1)
 P later                         1.3.0      2021-08-18 [?] CRAN (R 4.1.1)
 P lattice                       0.20-45    2021-09-22 [?] CRAN (R 4.1.1)
 P lazyeval                      0.2.2      2019-03-15 [?] CRAN (R 4.1.1)
 P leiden                        0.3.9      2021-07-27 [?] CRAN (R 4.1.1)
   leidenbase                    0.1.12     2022-09-29 [1] CRAN (R 4.1.1)
   lifecycle                     1.0.3      2022-10-07 [1] CRAN (R 4.1.1)
 P listenv                       0.8.0      2019-12-05 [?] CRAN (R 4.1.1)
   lme4                          1.1-31     2022-11-01 [1] CRAN (R 4.1.1)
 P lmtest                        0.9-39     2021-11-07 [?] CRAN (R 4.1.1)
 P magrittr                    * 2.0.1      2020-11-17 [?] CRAN (R 4.1.1)
 P MASS                          7.3-54     2021-05-03 [?] CRAN (R 4.1.1)
 P Matrix                      * 1.5-3      2022-11-11 [?] CRAN (R 4.1.1)
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 P memoise                       2.0.1      2021-11-26 [?] CRAN (R 4.1.1)
 P mgcv                          1.8-38     2021-10-06 [?] CRAN (R 4.1.1)
 P mime                          0.12       2021-09-28 [?] CRAN (R 4.1.1)
 P miniUI                        0.1.1.1    2018-05-18 [?] CRAN (R 4.1.1)
   minqa                         1.2.5      2022-10-19 [1] CRAN (R 4.1.1)
   monocle3                    * 1.3.1      2022-12-13 [1] Github (cole-trapnell-lab/monocle3@b545460)
 P motifmatchr                 * 1.16.0     2021-10-26 [?] Bioconductor
 P munsell                       0.5.0      2018-06-12 [?] CRAN (R 4.1.1)
 P nabor                       * 0.5.0      2018-07-11 [?] CRAN (R 4.1.1)
 P nlme                          3.1-153    2021-09-07 [?] CRAN (R 4.1.1)
   nloptr                        2.0.3      2022-05-26 [1] CRAN (R 4.1.1)
   parallelly                    1.32.1     2022-07-21 [1] CRAN (R 4.1.1)
 P patchwork                     1.1.1      2020-12-17 [?] CRAN (R 4.1.1)
 P pbapply                       1.5-0      2021-09-16 [?] CRAN (R 4.1.1)
 P pheatmap                      1.0.12     2019-01-04 [?] CRAN (R 4.1.1)
 P pillar                        1.6.4      2021-10-18 [?] CRAN (R 4.1.1)
 P pkgbuild                      1.2.1      2021-11-30 [?] CRAN (R 4.1.1)
 P pkgconfig                     2.0.3      2019-09-22 [?] CRAN (R 4.1.1)
 P pkgload                       1.2.4      2021-11-30 [?] CRAN (R 4.1.1)
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 P png                           0.1-7      2013-12-03 [?] CRAN (R 4.1.1)
 P polyclip                      1.10-0     2019-03-14 [?] CRAN (R 4.1.1)
 P poweRlaw                      0.70.6     2020-04-25 [?] CRAN (R 4.1.1)
 P pracma                        2.3.3      2021-01-23 [?] CRAN (R 4.1.1)
 P presto                        1.0.0      2021-12-08 [?] Github (immunogenomics/presto@052085d)
 P prettyunits                   1.1.1      2020-01-24 [?] CRAN (R 4.1.1)
 P processx                      3.5.2      2021-04-30 [?] CRAN (R 4.1.1)
 P progressr                     0.11.0     2022-09-02 [?] CRAN (R 4.1.1)
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   proxy                         0.4-27     2022-06-09 [1] CRAN (R 4.1.1)
 P ps                            1.6.0      2021-02-28 [?] CRAN (R 4.1.1)
 P purrr                         0.3.4      2020-04-17 [?] CRAN (R 4.1.1)
 P R.methodsS3                   1.8.1      2020-08-26 [?] CRAN (R 4.1.1)
 P R.oo                          1.24.0     2020-08-26 [?] CRAN (R 4.1.1)
 P R.utils                       2.11.0     2021-09-26 [?] CRAN (R 4.1.1)
 P R6                            2.5.1      2021-08-19 [?] CRAN (R 4.1.1)
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 P RColorBrewer                  1.1-2      2014-12-07 [?] CRAN (R 4.1.1)
 P Rcpp                        * 1.0.7      2021-07-07 [?] CRAN (R 4.1.1)
 P RcppAnnoy                     0.0.19     2021-07-30 [?] CRAN (R 4.1.1)
 P RcppArmadillo               * 0.10.7.3.0 2021-11-05 [?] CRAN (R 4.1.1)
 P RcppHNSW                      0.3.0      2020-09-06 [?] CRAN (R 4.1.1)
 P RCurl                         1.98-1.5   2021-09-17 [?] CRAN (R 4.1.1)
 P readr                         2.1.0      2021-11-11 [?] CRAN (R 4.1.1)
 P remotes                       2.4.2      2021-11-30 [?] CRAN (R 4.1.1)
   renv                          0.16.0     2022-09-29 [1] CRAN (R 4.1.1)
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 P restfulr                      0.0.13     2017-08-06 [?] CRAN (R 4.1.1)
 P reticulate                    1.22       2021-09-17 [?] CRAN (R 4.1.1)
 P rhandsontable                 0.3.8      2021-05-27 [?] CRAN (R 4.1.1)
 P rhdf5                       * 2.38.0     2021-10-26 [?] Bioconductor
 P rhdf5filters                  1.6.0      2021-10-26 [?] Bioconductor
 P Rhdf5lib                      1.16.0     2021-10-26 [?] Bioconductor
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   rlang                         1.0.6      2022-09-24 [1] CRAN (R 4.1.1)
 P rmarkdown                     2.18       2022-11-09 [?] CRAN (R 4.1.1)
 P ROCR                          1.0-11     2020-05-02 [?] CRAN (R 4.1.1)
 P rpart                         4.1-15     2019-04-12 [?] CRAN (R 4.1.1)
 P rprojroot                     2.0.2      2020-11-15 [?] CRAN (R 4.1.1)
 P Rsamtools                   * 2.10.0     2021-10-26 [?] Bioconductor
 P RSpectra                      0.16-0     2019-12-01 [?] CRAN (R 4.1.1)
 P RSQLite                       2.2.8      2021-08-21 [?] CRAN (R 4.1.1)
 P rstudioapi                    0.13       2020-11-12 [?] CRAN (R 4.1.1)
 P rtracklayer                 * 1.54.0     2021-10-26 [?] Bioconductor
 P Rtsne                         0.15       2018-11-10 [?] CRAN (R 4.1.1)
 P S4Vectors                   * 0.32.3     2021-11-21 [?] Bioconductor
 P sass                          0.4.0      2021-05-12 [?] CRAN (R 4.1.1)
 P scales                        1.1.1      2020-05-11 [?] CRAN (R 4.1.1)
 P scattermore                   0.7        2020-11-24 [?] CRAN (R 4.1.1)
 P sctransform                   0.3.2      2020-12-16 [?] CRAN (R 4.1.1)
 P seqLogo                       1.60.0     2021-10-26 [?] Bioconductor
 P sessioninfo                   1.2.1      2021-11-02 [?] CRAN (R 4.1.1)
 P Seurat                      * 4.0.5      2021-10-17 [?] CRAN (R 4.1.1)
 P SeuratObject                * 4.1.3      2022-11-07 [?] CRAN (R 4.1.1)
 P shape                         1.4.6      2021-05-19 [?] CRAN (R 4.1.1)
 P shiny                         1.7.1      2021-10-02 [?] CRAN (R 4.1.1)
 P SingleCellExperiment        * 1.16.0     2021-10-26 [?] Bioconductor
 P sp                            1.5-1      2022-11-07 [?] CRAN (R 4.1.1)
 P sparseMatrixStats           * 1.6.0      2021-10-26 [?] Bioconductor
 P spatstat.core                 2.3-1      2021-11-02 [?] CRAN (R 4.1.1)
 P spatstat.data                 2.1-0      2021-03-21 [?] CRAN (R 4.1.1)
 P spatstat.geom                 2.3-0      2021-10-09 [?] CRAN (R 4.1.1)
 P spatstat.sparse               2.0-0      2021-03-16 [?] CRAN (R 4.1.1)
 P spatstat.utils                2.2-0      2021-06-14 [?] CRAN (R 4.1.1)
 P stringi                       1.7.6      2021-11-29 [?] CRAN (R 4.1.1)
 P stringr                     * 1.4.0      2019-02-10 [?] CRAN (R 4.1.1)
 P SummarizedExperiment        * 1.24.0     2021-10-26 [?] Bioconductor
 P survival                      3.2-13     2021-08-24 [?] CRAN (R 4.1.1)
 P tensor                        1.5        2012-05-05 [?] CRAN (R 4.1.1)
   terra                         1.6-47     2022-12-02 [1] CRAN (R 4.1.1)
 P testthat                    * 3.1.1      2021-12-03 [?] CRAN (R 4.1.1)
 P TFBSTools                     1.32.0     2021-10-26 [?] Bioconductor
 P TFMPvalue                     0.0.8      2018-05-16 [?] CRAN (R 4.1.1)
 P tibble                        3.1.6      2021-11-07 [?] CRAN (R 4.1.1)
 P tidyr                         1.1.4      2021-09-27 [?] CRAN (R 4.1.1)
 P tidyselect                    1.1.1      2021-04-30 [?] CRAN (R 4.1.1)
 P tzdb                          0.2.0      2021-10-27 [?] CRAN (R 4.1.1)
 P usethis                     * 2.1.3      2021-10-27 [?] CRAN (R 4.1.1)
 P utf8                          1.2.2      2021-07-24 [?] CRAN (R 4.1.1)
 P uwot                        * 0.1.10     2020-12-15 [?] CRAN (R 4.1.1)
   vctrs                         0.5.1      2022-11-16 [1] CRAN (R 4.1.1)
   vipor                         0.4.5      2017-03-22 [1] CRAN (R 4.1.1)
 P viridisLite                   0.4.0      2021-04-13 [?] CRAN (R 4.1.1)
 P withr                         2.4.3      2021-11-30 [?] CRAN (R 4.1.1)
 P xfun                          0.35       2022-11-16 [?] CRAN (R 4.1.1)
 P XML                           3.99-0.8   2021-09-17 [?] CRAN (R 4.1.1)
 P xtable                        1.8-4      2019-04-21 [?] CRAN (R 4.1.1)
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 P yaml                          2.2.1      2020-02-01 [?] CRAN (R 4.1.1)
 P zlibbioc                      1.40.0     2021-10-26 [?] Bioconductor
 P zoo                           1.8-9      2021-03-09 [?] CRAN (R 4.1.1)

 [1] /corces/home/rcorces/ArchR/tutorial_221130/renv/library/R-4.1/x86_64-pc-linux-gnu
 [2] /corces/home/rcorces/ArchR/tutorial_221130/renv/sandbox/R-4.1/x86_64-pc-linux-gnu/3713ef1a

 P ── Loaded and on-disk path mismatch.
rcorces commented 1 year ago

closing as I cannot recapitulate this but please feel free to post again here if you have any update from your end. One other thing to try to look into this more would be to provide a PDF of the plot and open it in Adobe Illustrator to see if it is indeed a mask/additional layer on the plot or if it is something else.

Zepeng-Mu commented 1 year ago

Thanks. In fact the reason is the black border around heatmap cells that is covering everything. Setting rastr = F makes things better, I guess I can also increase raster quality in ComplexHeatmap.