Gene Orientation not correct

[xyz0o]

I have specified the strand orientation in the table as forward= 1 and reverse= -1 and I use below command to draw my genes

ggplot(dfg, aes(xmin = start, xmax = end, y = Gene, fill = element, label = element,
                          forward = orientation)) +
  geom_gene_arrow() +
  facet_wrap(~ Gene, scales = "free", ncol = 1) +
  scale_fill_brewer(palette = "Set3") +
  geom_blank(data = dfg, aes(forward = 1)) +
  theme_genes()

my problem is the figure returns incorrect orientation in relation to the upstream, downstream elements that I have. For example:

<style> </style>

Ltn1	stop_codon	16353834	16353837	reverse	-1
Ltn1	exon	16353837	16353954	reverse	-1
Ltn1	intron	16353954	16354032	reverse	-1
Ltn1	exon	16354032	16354473	reverse	-1
Ltn1	intron	16354473	16354532	reverse	-1
Ltn1	exon	16354532	16354808	reverse	-1
Ltn1	intron	16354808	16354878	reverse	-1
Ltn1	exon	16354878	16355062	reverse	-1
Ltn1	intron	16355062	16355118	reverse	-1
Ltn1	exon	16355118	16355351	reverse	-1
Ltn1	intron	16355351	16355406	reverse	-1
Ltn1	exon	16355406	16356726	reverse	-1
Ltn1	intron	16356726	16357235	reverse	-1
Ltn1	exon	16357235	16358277	reverse	-1
Ltn1	intron	16358277	16358363	reverse	-1
Ltn1	exon	16358363	16358543	reverse	-1
Ltn1	intron	16358543	16358602	reverse	-1
Ltn1	exon	16358602	16359381	reverse	-1
Ltn1	intron	16359381	16359443	reverse	-1
Ltn1	exon	16359443	16359491	reverse	-1
Ltn1	start_codon	16359488	16359491	reverse	-1
Ltn1	TE	16353156	16353284	reverse	-1

TE should be placed before the first exon based on the coordinates (downstream) but instead it is drawn as an "upstream" element:

I got this problem since I had to re-install the package.

[wilkox]

Because -1 coerces to the logical value TRUE, setting orientation as -1 is the same as setting forward = TRUE. If you replace it with 0, you should get the expected result:

library(tidyverse)
library(gggenes)

dfg <- tribble(
  ~gene, ~element, ~start, ~end, ~strand, ~orientation,
  "Ltn1",   "stop_codon",   16353834,   16353837,   "reverse",  0,
  "Ltn1",   "exon", 16353837,   16353954,   "reverse",  0,
  "Ltn1",   "intron",   16353954,   16354032,   "reverse",  0,
  "Ltn1",   "exon", 16354032,   16354473,   "reverse",  0,
  "Ltn1",   "intron",   16354473,   16354532,   "reverse",  0,
  "Ltn1",   "exon", 16354532,   16354808,   "reverse",  0,
  "Ltn1",   "intron",   16354808,   16354878,   "reverse",  0,
  "Ltn1",   "exon", 16354878,   16355062,   "reverse",  0,
  "Ltn1",   "intron",   16355062,   16355118,   "reverse",  0,
  "Ltn1",   "exon", 16355118,   16355351,   "reverse",  0,
  "Ltn1",   "intron",   16355351,   16355406,   "reverse",  0,
  "Ltn1",   "exon", 16355406,   16356726,   "reverse",  0,
  "Ltn1",   "intron",   16356726,   16357235,   "reverse",  0,
  "Ltn1",   "exon", 16357235,   16358277,   "reverse",  0,
  "Ltn1",   "intron",   16358277,   16358363,   "reverse",  0,
  "Ltn1",   "exon", 16358363,   16358543,   "reverse",  0,
  "Ltn1",   "intron",   16358543,   16358602,   "reverse",  0,
  "Ltn1",   "exon", 16358602,   16359381,   "reverse",  0,
  "Ltn1",   "intron",   16359381,   16359443,   "reverse",  0,
  "Ltn1",   "exon", 16359443,   16359491,   "reverse",  0,
  "Ltn1",   "start_codon",  16359488,   16359491,   "reverse",  0,
  "Ltn1",   "TE",   16353156,   16353284,   "reverse",  0)

ggplot(dfg, aes(xmin = start, xmax = end, y = gene, fill = element, label = element, forward = orientation)) +
  geom_gene_arrow() +
  facet_wrap(~ gene, scales = "free", ncol = 1) +
  scale_fill_brewer(palette = "Set3") +
  geom_blank(data = dfg, aes(forward = 1)) +
  theme_genes()

^{Created on 2023-11-14 with reprex v2.0.2}