Calculate the direction of data obtained from gff file

[cabraham03]

Calculate the direction of data obtained from gff file

[cabraham03]

Thanks So Much !!!

[wilkox]

Hi @cabraham03, do you want to change the direction of individual genes (this is controlled by the forward aesthetic), or reverse the direction of the entire locus shown in Genome-320 so that it resembles Genome-300?

[cabraham03]

Hello.
not for a single gene, all the genes in the second plot (Genome-320), I found this solution, but I'm not sure:
if I have a full length of 150 bp (just an example), and I have 2 genes, geneA start at 10 (start1) and end at 50 bp (end1), and geneB start at 80 (start1) and end at 130 bp (end1); so, to calculate the genes direction will be:
start2 = (total length - end1) +1
end2 = (total length - start1) + 1

so
geneA
start2= (150-50) + 1=101
end2 = (150-10)+1 = 141

geneB
start2 = (150 - 130) + 1 = 21
end2 = (150 - 80) + 1 = 71

is it ok ?
thanks !!!

[wilkox]

I think the best way to do it would be to draw the genomes separately with the x-axis reversed for Genome-320, then composite the plots with patchwork. This way you avoid showing incorrect coordinates for the genes.

# Libraries
library(tidyverse)
library(gggenes)
library(patchwork)

# Data
df <- tribble(
  ~file_id,     ~seq_id,        ~start, ~end,   ~strand, ~feat_id,         ~locus_tag,       ~orientation, ~gene,      ~cluster,        ~position,
  "Genome-300", "Genome-300_1", 199743, 201911, "-",     "IMEHDJCA_00189", "IMEHDJCA_00189", -1,           "geneE",    "cluster_00365", 200827,
  "Genome-300", "Genome-300_1", 201914, 203275, "-",     "IMEHDJCA_00190", "IMEHDJCA_00190", -1,           "geneD",    "cluster_01313", 202594,
  "Genome-300", "Genome-300_1", 203272, 205377, "-",     "IMEHDJCA_00191", "IMEHDJCA_00191", -1,           "geneB",    "cluster_00403", 204324,
  "Genome-300", "Genome-300_1", 205817, 206176, "+",     "IMEHDJCA_00192", "IMEHDJCA_00192",  1,           "gene1033", "cluster_06099", 205996,
  "Genome-300", "Genome-300_1", 206268, 206663, "+",     "IMEHDJCA_00193", "IMEHDJCA_00193",  1,           "geneC",    "cluster_05858", 206465,
  "Genome-300", "Genome-300_1", 206686, 222306, "+",     "IMEHDJCA_00194", "IMEHDJCA_00194",  1,           "geneA",    "cluster_00001", 214496,
  "Genome-320", "Genome-320_8", 123699, 139310, "-",     "ILCJGNBA_01570", "ILCJGNBA_01570", -1,           "geneA",    "cluster_00001", 131504,
  "Genome-320", "Genome-320_8", 139333, 139728, "-",     "ILCJGNBA_01571", "ILCJGNBA_01571", -1,           "geneC",    "cluster_05858", 139530,
  "Genome-320", "Genome-320_8", 139820, 140179, "-",     "ILCJGNBA_01572", "ILCJGNBA_01572", -1,           "gene1033", "cluster_06099", 139999,
  "Genome-320", "Genome-320_8", 140619, 142724, "+",     "ILCJGNBA_01573", "ILCJGNBA_01573",  1,           "geneB",    "cluster_00403", 141671,
  "Genome-320", "Genome-320_8", 142721, 144082, "+",     "ILCJGNBA_01574", "ILCJGNBA_01574",  1,           "geneD",    "cluster_01322", 143401,
  "Genome-320", "Genome-320_8", 144085, 146253, "+",     "ILCJGNBA_01575", "ILCJGNBA_01575",  1,           "geneE",    "cluster_00365", 145169
)

# Convert orientation to logical
df$orientation <- ifelse(df$orientation == 1, TRUE, FALSE)

# Plot
base <- ggplot(df, aes(xmin = start, xmax = end, y = file_id, fill = gene)) +
  scale_fill_manual(values = c("orange", "blue", "red",  "green", "yellow", "#878787")) +
  scale_y_discrete(position = "right") +
  gggenes::theme_genes() +
  theme(panel.background = element_rect(fill = 'white' , color = 'white' ),
        panel.grid.major.y = ggplot2::element_line(colour = "grey", linewidth = 0.6),
        axis.title.y= element_blank(), 
        axis.text.y = element_text(size = 14, # sample name size
                                   family="Times New Roman", 
                                   face="bold")
  )

genome300 <- base + geom_gene_arrow(
  data = df[which(df$file_id == "Genome-300"), ],
  aes(forward = orientation),
  arrow_body_height = unit(7, "mm"),
  arrowhead_height = unit(7, "mm"),
  arrowhead_width = unit(5.7, "mm")
)

genome320 <- base + geom_gene_arrow(
  data = df[which(df$file_id == "Genome-320"), ],
  aes(forward = orientation),
  arrow_body_height = unit(7, "mm"),
  arrowhead_height = unit(7, "mm"),
  arrowhead_width = unit(5.7, "mm")
) + scale_x_continuous(transform = "reverse")

(genome300 / genome320) + plot_layout(guides = "collect")

^{Created on 2024-05-28 with reprex v2.1.0}