I am trying to create a Chord diagram in R using the circlize package by following the examples from https://jokergoo.github.io/circlize_book/book/legends.html. This works fine, but I run into errors trying to insert some figure legends using the gridbase and Complexheatmap R packages.
I am supposed to set the "omi" parameter using par(omi = gridOMI(), new = TRUE). Unfortunately, par does not seem to recognize the vector created by gridOMI() as correct input and I don't know why.
The code I have is this:
library(circlize)
library(ComplexHeatmap)
library(tidyverse)
library(gridBase)
library(grid)
df <- structure(list(term_name = c("cats", "dogs", "goldfish", "hamster",
"quinea pig", "snake", "cats", "quinea pig", "capybara", "quinea pig",
"snake", "cats", "cats", "cats", "dogs", "goldfish", "dogs",
"goldfish", "dogs", "goldfish", "dogs", "goldfish", "dogs", "goldfish",
"capybara", "dogs", "goldfish", "dogs", "goldfish", "goldfish"
), Gene = c("A1", "A2", "A2", "A2", "A2", "A3", "A3", "A4", "B1",
"B2", "B3", "B3", "B4", "B5", "B6", "B6", "B7", "B7", "B8", "B8",
"C1", "C1", "C2", "C2", "C3", "C4", "C4", "C5", "C5", "C6"),
adjusted_p_value = c(0.0401123837727216, 0.00599293759030441,
0.008037018541932, 0.0238949037996737, 0.0455988630423016,
0.0362906272864953, 0.0401123837727216, 0.0455988630423016,
0.0175800574990072, 0.0455988630423016, 0.0362906272864953,
0.0401123837727216, 0.0401123837727216, 0.0401123837727216,
0.00599293759030441, 0.008037018541932, 0.00599293759030441,
0.008037018541932, 0.00599293759030441, 0.008037018541932,
0.00599293759030441, 0.008037018541932, 0.00599293759030441,
0.008037018541932, 0.0175800574990072, 0.00599293759030441,
0.008037018541932, 0.00599293759030441, 0.008037018541932,
0.008037018541932), FoldChange = c(9.65818273715244, 8.77862464376709,
8.77862464376709, 8.77862464376709, 8.77862464376709, 8.56731315195869,
8.56731315195869, 8.43444706073958, 8.12991568737931, 8.12449961176595,
8.08270580330019, 8.08270580330019, 8.02040115004825, 8.00996652274416,
7.64451918356123, 7.64451918356123, 7.2756458952698, 7.2756458952698,
6.14815597897133, 6.14815597897133, 5.8393823870724, 5.8393823870724,
5.70624023824579, 5.70624023824579, 5.31939602787647, 5.14071417928765,
5.14071417928765, 5.00924279397654, 5.00924279397654, 4.87034859437948
)), row.names = c(NA, -30L), class = c("tbl_df", "tbl", "data.frame"
))
### Chord diagram code
# create color ranges for visualization
col_fun_pval = colorRamp2(c(min(df$adjusted_p_value), mean(df$adjusted_p_value), max(df$adjusted_p_value)), c("magenta", "green", "blue"))
#col_fun_FC = colorRamp2(range(df$FoldChange), c("#FFE6E6", "#FF0000"))
col_fun_FC = colorRamp2(range(df$FoldChange), c("#b38f00", "#fffae6"))
# map grid color values to Fold change values. GO grid color set to adjusted P-val.
gene_names <- unique(df$Gene)
Foldchange <- df$FoldChange[!duplicated(df$Gene)]
names(Foldchange) <- gene_names
GO_names <- unique(df$term_name)
GO_col <- df$adjusted_p_value[!duplicated(df$term_name)]
names(GO_col) <- GO_names
grid.col = c(col_fun_pval(GO_col), col_fun_FC(Foldchange))
#define Chord diagram plot function
Chord_plot <- function() {
circos.par(gap.after = c(rep(6, length(unique(df[[1]]))-1), 10,
rep(1, length(unique(df[[2]]))-1), 10),
clock.wise = FALSE, start.degree = 180)
chordDiagram(df[, 1:2],
col = col_fun_pval(df[, 3]), grid.col = grid.col, annotationTrack = "grid",
directional = 1, link.border = NA, preAllocateTracks = list(track.height = max(strwidth(gene_names))))
# we go back to the first track and customize sector labels
circos.track(track.index = 1, panel.fun = function(x, y) {
if (CELL_META$sector.index %in% gene_names) {
circos.text(CELL_META$xcenter, CELL_META$ylim[1], CELL_META$sector.index,
facing = "clockwise", niceFacing = TRUE, adj = c(0, 0.5), cex = 0.8)
}
}, bg.border = NA) # here set bg.border to NA is important
circos.clear()
}
# create continuous legends
dig_num <- 2
lgd_FC = Legend(at = c(round(min(Foldchange), digits = dig_num),
round(min(Foldchange) + (1/4*(max(Foldchange - min(Foldchange)))), digits = dig_num),
round(min(Foldchange) + (2/4*(max(Foldchange - min(Foldchange)))), digits = dig_num),
round(min(Foldchange) + (3/4*(max(Foldchange - min(Foldchange)))), digits = dig_num),
round(min(Foldchange) + (4/4*(max(Foldchange - min(Foldchange)))), digits = dig_num)),
col_fun = col_fun_FC,
title_position = "topleft", title = "Fold Change")
lgd_pval = Legend(at = c(round(min(GO_col), digits = dig_num),
round(min(GO_col) + (1/4*(max(GO_col - min(GO_col)))), digits = dig_num),
round(min(GO_col) + (2/4*(max(GO_col - min(GO_col)))), digits = dig_num),
round(min(GO_col) + (3/4*(max(GO_col - min(GO_col)))), digits = dig_num),
round(min(GO_col) + (4/4*(max(GO_col - min(GO_col)))), digits = dig_num)),
col_fun = col_fun_pval,
title_position = "topleft", title = "GO p-value")
# stack legends
lgd_list_vertical = packLegend(lgd_FC, lgd_pval)
### use gridbase to plot legends and chorddiagram
plot.new()
circle_size = unit(1, "snpc") # snpc unit gives you a square region
pushViewport(viewport(x = 0, y = 0.5, width = circle_size, height = circle_size,
just = c("left", "center")))
par(omi = gridOMI(), new = TRUE)
Chord_plot()
upViewport()
draw(lgd_list_vertical, x = circle_size, just = "left")
Trying to run the above code gives the following error
Error in par(omi = gridOMI(), new = TRUE) :
invalid value specified for graphical parameter "omi"
I don't know if it is a problem with my R version, package versions, package conflicts or something different. By googling I couldn't find anyone with the same problem.
Just in case it is important, here are the details from sessioninfo()
R version 4.2.0 (2022-04-22 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 22000)
Matrix products: default
locale:
[1] LC_COLLATE=Dutch_Netherlands.utf8 LC_CTYPE=Dutch_Netherlands.utf8 LC_MONETARY=Dutch_Netherlands.utf8 LC_NUMERIC=C
[5] LC_TIME=Dutch_Netherlands.utf8
attached base packages:
[1] grid stats graphics grDevices utils datasets methods base
other attached packages:
[1] gridBase_0.4-7 forcats_0.5.2 stringr_1.4.1 dplyr_1.0.10 purrr_0.3.4 readr_2.1.2 tidyr_1.2.1
[8] tibble_3.1.8 ggplot2_3.3.6 tidyverse_1.3.2 ComplexHeatmap_2.12.1 circlize_0.4.15
loaded via a namespace (and not attached):
[1] httr_1.4.4 bit64_4.0.5 vroom_1.5.7 jsonlite_1.8.0 foreach_1.5.2 modelr_0.1.9 assertthat_0.2.1 stats4_4.2.0
[9] googlesheets4_1.0.1 cellranger_1.1.0 yaml_2.3.5 pillar_1.8.1 backports_1.4.1 glue_1.6.2 digest_0.6.29 RColorBrewer_1.1-3
[17] rvest_1.0.3 colorspace_2.0-3 htmltools_0.5.3 pkgconfig_2.0.3 GetoptLong_1.0.5 broom_1.0.1 haven_2.5.1 scales_1.2.1
[25] tzdb_0.3.0 googledrive_2.0.0 generics_0.1.3 IRanges_2.30.0 ellipsis_0.3.2 withr_2.5.0 BiocGenerics_0.42.0 cli_3.3.0
[33] magrittr_2.0.3 crayon_1.5.1 readxl_1.4.1 evaluate_0.16 fs_1.5.2 fansi_1.0.3 doParallel_1.0.17 xml2_1.3.3
[41] tools_4.2.0 hms_1.1.2 GlobalOptions_0.1.2 gargle_1.2.1 lifecycle_1.0.2 matrixStats_0.62.0 S4Vectors_0.34.0 munsell_0.5.0
[49] reprex_2.0.2 cluster_2.1.3 compiler_4.2.0 rlang_1.0.6 iterators_1.0.14 rstudioapi_0.14 rjson_0.2.21 rmarkdown_2.16
[57] gtable_0.3.1 codetools_0.2-18 DBI_1.1.3 R6_2.5.1 lubridate_1.8.0 knitr_1.40 fastmap_1.1.0 bit_4.0.4
[65] utf8_1.2.2 clue_0.3-61 shape_1.4.6 stringi_1.7.8 parallel_4.2.0 vctrs_0.4.1 png_0.1-7 xfun_0.33
[73] dbplyr_2.2.1 tidyselect_1.1.2
Any help would be really appreciated, as I am kind of stuck on this error.
EDIT: I found out I do not get this error in another system. If I do sessioninfo() there, I get the following outout
R version 4.1.1 (2021-08-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)
Matrix products: default
BLAS: /sw/apps/R/4.1.1/rackham/lib64/R/lib/libRblas.so
LAPACK: /sw/apps/R/4.1.1/rackham/lib64/R/lib/libRlapack.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8
[4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] grid stats graphics grDevices utils datasets methods base
other attached packages:
[1] gridBase_0.4-7 forcats_0.5.1 stringr_1.4.0 dplyr_1.0.7
[5] purrr_0.3.4 readr_2.0.2 tidyr_1.1.4 tibble_3.1.5
[9] ggplot2_3.3.5 tidyverse_1.3.1 circlize_0.4.13 ComplexHeatmap_2.8.0
loaded via a namespace (and not attached):
[1] Rcpp_1.0.7 lubridate_1.8.0 png_0.1-7 assertthat_0.2.1
[5] digest_0.6.28 foreach_1.5.1 utf8_1.2.2 R6_2.5.1
[9] cellranger_1.1.0 backports_1.3.0 reprex_2.0.1 stats4_4.1.1
[13] httr_1.4.2 pillar_1.6.4 GlobalOptions_0.1.2 rlang_0.4.12
[17] readxl_1.3.1 rstudioapi_0.13 S4Vectors_0.30.2 GetoptLong_1.0.5
[21] munsell_0.5.0 broom_0.7.10 compiler_4.1.1 modelr_0.1.8
[25] pkgconfig_2.0.3 BiocGenerics_0.38.0 shape_1.4.6 tidyselect_1.1.1
[29] IRanges_2.26.0 codetools_0.2-18 matrixStats_0.61.0 fansi_0.5.0
[33] crayon_1.4.2 tzdb_0.1.2 dbplyr_2.1.1 withr_2.4.2
[37] jsonlite_1.7.2 gtable_0.3.0 lifecycle_1.0.1 DBI_1.1.1
[41] magrittr_2.0.1 scales_1.1.1 cli_3.1.0 stringi_1.7.5
[45] fs_1.5.0 doParallel_1.0.16 xml2_1.3.2 ellipsis_0.3.2
[49] generics_0.1.1 vctrs_0.3.8 rjson_0.2.20 RColorBrewer_1.1-2
[53] iterators_1.0.13 tools_4.1.1 Cairo_1.5-12.2 glue_1.5.0
[57] hms_1.1.1 parallel_4.1.1 clue_0.3-60 colorspace_2.0-2
[61] cluster_2.1.2 rvest_1.0.2 haven_2.4.3
I hope this helps. The main differences I notice is the R version, which is older on this system, and the locale.
I found one solution. gridOMI() is apparantly sensitive to Rstudio's zoom function, which resizes the text and user-interface elements. For me, gridOMI() gave an invalid value, because I my user-interface elements were too small.
You can resize Rstudio's text and user-interface elements by clicking on zoom in or zoom out in the View menu.