Need help in plotting RNA-seq foldchange values in circos plot
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pooja • 0
@42f335fd
Last seen 2 days ago
United States

Hi All,

```library(circlize)
   library(gtools)
   library(dplyr)
  circos.initializeWithIdeogram(species = "mm10")
  circos.par("track.height"=0.20)

  circos.genomicTrackPlotRegion(data = db_tr,ylim = c(-7,7), numeric.column = 4,
  panel.fun = function(region,value,...) {
  cond <- value[,1] < 0.0
  circos.genomicPoints(region[cond,], value[cond,], pch = ".", cex = 0.1,
  col = "khaki4")
  circos.genomicPoints(region[!cond,], value[!cond,], pch = ".", cex = 0.1,
  col = "indianred")
  })

My input data has the following format: Chrom start_pos end_pos value

 14 20482867    20496901    2.713009346
 4     123712710    123718202   -2.20797815
13    80883384  80896042    1.646405782
16  48842551    48844461    -1.636002557
17  28399094    28517527    1.033066311
 9  31846044    31913462    -1.738549101
 1  45311538    45349706    -1.360867536

The problem I am facing is that the code is working but it is not plotting the genomic points as mentioned in the code as khaki and red color. If anybody knows or have any idea about resolving this issue then please help. Any kind of help in this regard will be highly appreciated.

Thanks in advance.

sessionInfo( )

``` R version 4.1.1 (2021-08-10) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 7 x64 (build 7601) Service Pack 1

Matrix products: default

locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C LC_TIME=English_United States.1252

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

other attached packages: [1] dplyr_1.0.7 gtools_3.9.2 circlize_0.4.13

loaded via a namespace (and not attached): [1] fansi_0.5.0 assertthat_0.2.1 crayon_1.4.1 utf8_1.2.2 grid_4.1.1
[6] R6_2.5.1 DBI_1.1.1 lifecycle_1.0.1 magrittr_2.0.1 pillar_1.6.3
[11] rlang_0.4.11 GlobalOptions_0.1.2 vctrs_0.3.8 generics_0.1.0 ellipsis_0.3.2
[16] tools_4.1.1 glue_1.4.2 purrr_0.3.4 compiler_4.1.1 pkgconfig_2.0.3
[21] colorspace_2.0-2 shape_1.4.6 tidyselect_1.1.1 tibble_3.1.4

Circos • 83 views
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