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White lines in Oncoprints - Rasterization issue? #1210

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w2felix opened this issue Oct 17, 2024 · 0 comments
Open

White lines in Oncoprints - Rasterization issue? #1210

w2felix opened this issue Oct 17, 2024 · 0 comments

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@w2felix
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w2felix commented Oct 17, 2024

I have an issue with Oncoprints, which has been described here (#621) but did not solve my issue:

ComplexHeatmap 2.21.0, magick installed

I tried to follow all suggestions like:
use_raster = TRUE, raster_by_magick = TRUE

but that did not help and also turning rastering of produced the same white lines:
use_raster = F

when I have small width, the top anno does not look nice (n = 514, no NA entries, so this should not be the reason):
image

As soon as I increase the width:
image
image
image

library(ComplexHeatmap)

col = c(`>100 TPM` = "darkgreen")

alter_fun = list(
  background = alter_graphic("rect", fill = "lightgrey"),   
  `>100 TPM` = alter_graphic("rect", width = 1, horiz_margin = unit(0, "pt"), fill = col[">100 TPM"])
)

oncoPrint(oncoprint_data,
           alter_fun = alter_fun,
           col = col,
           row_order = 1:nrow(oncoprint_data), 
           right_annotation = NULL,
           row_names_side = "left",
           pct_side = "right",
           use_raster = TRUE)

sessionInfo()
> sessionInfo()
R version 4.4.0 (2024-04-24 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 10 x64 (build 19045)

Matrix products: default


locale:
[1] LC_COLLATE=German_Germany.utf8  LC_CTYPE=German_Germany.utf8    LC_MONETARY=German_Germany.utf8 LC_NUMERIC=C                   
[5] LC_TIME=German_Germany.utf8    

time zone: Europe/Berlin
tzcode source: internal

attached base packages:
[1] grid      stats     graphics  grDevices datasets  utils     methods   base     

other attached packages:
 [1] ComplexHeatmap_2.21.1 lubridate_1.9.3       forcats_1.0.0         stringr_1.5.1         dplyr_1.1.4           purrr_1.0.2          
 [7] readr_2.1.5           tidyr_1.3.1           tibble_3.2.1          ggplot2_3.5.1         tidyverse_2.0.0      

loaded via a namespace (and not attached):
 [1] utf8_1.2.4          generics_0.1.3      renv_1.0.7          shape_1.4.6.1       stringi_1.8.4       hms_1.1.3           digest_0.6.37      
 [8] magrittr_2.0.3      RColorBrewer_1.1-3  timechange_0.3.0    iterators_1.0.14    circlize_0.4.16     foreach_1.5.2       doParallel_1.0.17  
[15] GlobalOptions_0.1.2 BiocManager_1.30.25 fansi_1.0.6         scales_1.3.0        codetools_0.2-20    cli_3.6.3           rlang_1.1.4        
[22] crayon_1.5.3        munsell_0.5.1       withr_3.0.1         tools_4.4.0         parallel_4.4.0      tzdb_0.4.0          colorspace_2.1-1   
[29] GetoptLong_1.0.5    BiocGenerics_0.50.0 vctrs_0.6.5         R6_2.5.1            png_0.1-8           stats4_4.4.0        matrixStats_1.4.1  
[36] lifecycle_1.0.4     S4Vectors_0.42.1    IRanges_2.38.1      clue_0.3-65         cluster_2.1.6       pkgconfig_2.0.3     pillar_1.9.0       
[43] gtable_0.3.5        glue_1.8.0          tidyselect_1.2.1    rstudioapi_0.17.0   rjson_0.2.23        compiler_4.4.0     
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