I used the R package circlize to draw a PDF image (Figure 1)fig.1. The display of images viewed through R studio zoom and WPS(a type of PDF reader) is shown in Figure 1. However, when I opened the PDF through AI, a large number of redundant lines appeared, as shown in Figure 2fig.2. The details of redundant lines were shown in Figure 3fig3. What is the reason? How to solve it?
The body code of my drawing is as follows (some coloring related code or data are not shown)：
library(circlize)
library(reshape2)
library(ComplexHeatmap)
library(grid)
library(dplyr)
library(tidyr)
gap_size <- c(rep(0.8, length(all_otu) - 1), 6, rep(0.8, length(all_sample) - 1), 6)
circos.par(cell.padding = c(0, 0, 0, 0), start.degree = 270, gap.degree = gap_size)
circos.initialize(factors = factor(all_ID, levels = all_ID), xlim = all_ID_xlim)
circos.trackPlotRegion(
ylim = c(0, 1), track.height = 0.03,
bg.border = NA,
panel.fun = function(x, y) {
sector.index = get.cell.meta.data('sector.index')
xlim = get.cell.meta.data('xlim')
ylim = get.cell.meta.data('ylim')
} )
for (i in 1:length(tax_phylum)) {
tax_OTU <- {subset(taxonomy, phylum == tax_phylum[i])}$OTU_ID
highlight.sector(tax_OTU, track.index = 1, col = color_otu[i],
text = tax_phylum[i],
facing = "clockwise",cex = 0.5, text.col = 'black', niceFacing = T)
}
for (i in 1:length(all_group)) {
group_sample <- {subset(group, group_ID == all_group[i])}$sample_ID
highlight.sector(group_sample, track.index = 1, col = color_sample[i],
text = all_group[i],
facing = "clockwise",cex = 0.7, text.col = 'black',niceFacing = T)
}
link_color <- character(nrow(plot_data))
for (i in seq_len(nrow(plot_data))) {
group_index <- match(plot_data[i,1], group[,1])
color_index <- group[group_index, 2]
link_color[i] <- color_sample[color_index]
circos.link(
plot_data[i,1], c(accum_sample[as.character(plot_data[i,1])], accum_sample[as.character(plot_data[i,1])] - plot_data[i,4]),
plot_data[i,2], c(accum_otu[as.character(plot_data[i,2])], accum_otu[as.character(plot_data[i,2])] - plot_data[i,3]),
#col = paste0(color_otu[plot_data[i,2]], '70'), border = NA )
col = paste0(link_color[i], '75'), border = NA )
accum_otu[as.character(plot_data[i,2])] = accum_otu[as.character(plot_data[i,2])] - plot_data[i,4]
accum_sample[as.character(plot_data[i,1])] = accum_sample[as.character(plot_data[i,1])] - plot_data[i,3]
}
all_ID,chr[1:156]
> all_ID
[1] "hg_bin.256"
[2] "fg_bin.37"
[3] "hg_bin.189"
[4] "hg_bin.230"
[5] "hg_bin.257"
all_ID_xlim,156 obs. of 2 variables
> all_ID_xlim rep(0, length(all_ID))
hg_bin.256 0
fg_bin.37 0
hg_bin.189 0
hg_bin.230 0
hg_bin.257 0
hg_bin.258 0
hg_bin.112 0
plot_data,6075 obs. of 4 variables
> head(plot_data)
sample_ID otu_ID value value.1
1 aminoglycoside__aac(2')-I hg_bin.256 0 0
82 aminoglycoside__aac(3)-I hg_bin.256 0 0
163 bacitracin__bacA hg_bin.256 1 1
244 beta-lactam__ampC hg_bin.256 0 0
325 beta-lactam__CfxA2 hg_bin.256 0 0
406 beta-lactam__CfxA3 hg_bin.256 0 0
tax_phylum
> tax_phylum
[1] p__Firmicutes_A p__Bacteroidota p__Proteobacteria
[4] other p__Actinobacteriota p__Firmicutes
[7] p__Planctomycetota p__Cyanobacteria p__Firmicutes_C
[10] p__Fusobacteriota
10 Levels: p__Firmicutes_A p__Bacteroidota p__Proteobacteria ... p__Fusobacteriota
all_group,chr[1:16]
> head(all_group)
[1] "aminoglycoside" "bacitracin" "beta-lactam"
[4] "chloramphenicol" "fosfomycin" "fosmidomycin"
group，75 obs. of 2 variables
> head(group)
sample_ID group_ID
1 aminoglycoside__aac(2')-I aminoglycoside
2 aminoglycoside__aac(3)-I aminoglycoside
3 bacitracin__bacA bacitracin
4 beta-lactam__ampC beta-lactam
5 beta-lactam__CfxA2 beta-lactam
6 beta-lactam__CfxA3 beta-lactam
taxonomy，81 obs. of 8 variables
> head(taxonomy)
OTU_ID kingdom phylum class
2 hg_bin.256 d__Bacteria p__Firmicutes_A c__Clostridia
4 fg_bin.37 d__Bacteria p__Firmicutes_A c__Clostridia
14 hg_bin.189 d__Bacteria p__Firmicutes_A c__Clostridia
16 hg_bin.230 d__Bacteria p__Firmicutes_A c__Clostridia
18 hg_bin.257 d__Bacteria p__Firmicutes_A c__Clostridia
19 hg_bin.258 d__Bacteria p__Firmicutes_A c__Clostridia
order family genus
2 o__Lachnospirales f__Lachnospiraceae g__Eubacterium_G
4 o__Lachnospirales f__Lachnospiraceae g__Acetatifactor
14 o__Lachnospirales f__Lachnospiraceae g__CAG-510
16 o__Lachnospirales f__Lachnospiraceae g__Dorea_A
18 o__Lachnospirales f__Lachnospiraceae g__Eubacterium_G
19 o__Oscillospirales f__Acutalibacteraceae g__Eubacterium_R
species
2 s__Eubacterium_G sp000434315
4 s__Acetatifactor intestinalis
14 s__CAG-510 sp000434615
16 s__Dorea_A longicatena_B
18 s__Eubacterium_G ventriosum
19 s__Eubacterium_R sp000434995
At the same time, I also tried to export the file in eps format using R studio and open it using AI. The AI suggested that I lacked Helvetica font and all lines were not displayed (see Figure 4)fig4. After I installed Helvetica font and opened it using AI, no font error was reported, but the image preview was still the same as that in Figure 4.
When I use the example data and the example code, there are no redundant lines, so I am more confident that it is my code error, or my own data overload？
