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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
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
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):
As soon as I increase the width:
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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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):
As soon as I increase the width:
The text was updated successfully, but these errors were encountered: