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