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Adjustments to ribbon plots R script #44

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Merged
lcoombe merged 1 commit into from
May 10, 2024
Merged

Adjustments to ribbon plots R script #44

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10 changes: 5 additions & 5 deletions visualization_scripts/plot_synteny_blocks_gggenomes.R
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Original file line number Diff line number Diff line change
Expand Up @@ -18,15 +18,15 @@ parser$add_argument("-p", "--prefix",

args <- parser$parse_args()


# Read in and prepare sequences
sequences <- read.csv(args$sequences, sep = "\t", header = TRUE)

# https://stackoverflow.com/questions/32378108/using-gtoolsmixedsort-or-alternatives-with-dplyrarrange
input_order <- unique(sequences$bin_id)
input_chrom_order <- unique(sequences$seq_id)
mixedrank <- function(x) order(gtools::mixedorder(x))
sequences <- sequences %>%
arrange(factor(bin_id, levels=input_order), mixedrank(seq_id))
arrange(factor(bin_id, levels=input_order), factor(seq_id, levels=input_chrom_order))


# Read in and prepare synteny links
Expand Down Expand Up @@ -54,16 +54,16 @@ if (args$scale %% 1e9 == 0) {

# Make the ribbon plot - these layers can be fully customized as needed!
make_plot <- function(links, sequences, add_scale_bar = FALSE) {

num_colours <- length(unique(links$colour_block))
p <- gggenomes(seqs = sequences, links = links)
plot <- p + theme_gggenomes_clean(base_size = 15) +
geom_link(aes(fill = colour_block), offset = 0, alpha = 0.5) +
geom_link(aes(fill = colour_block), offset = 0, alpha = 0.5, size = 0.05) +
geom_seq(size = 2, colour = "grey") + # draw contig/chromosome lines
geom_bin_label(aes(label = bin_id), size = 6, hjust = 0.9) + # label each bin
#geom_seq_label(aes(label = seq_id), vjust = 1.1, size = 4) + # Can add seq labels if desired
theme(axis.text.x = element_text(size = 25),
legend.position = "bottom") +
scale_fill_manual(values = hue_pal()(length(unique(links$seq_id))),
scale_fill_manual(values = hue_pal()(num_colours),
breaks = unique(links$seq_id)) +
scale_colour_manual(values = c("red")) +
guides(fill = guide_legend(title = "", ncol = 10),
Expand Down