## ---- echo = FALSE-------------------------------------------------------
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.width = 6,
  fig.height = 10
)

## ----geom_gene_arrow, message = FALSE------------------------------------
library(ggplot2)
library(gggenes)
ggplot(example_genes, aes(xmin = start, xmax = end, y = molecule, fill = gene)) +
  geom_gene_arrow() +
  facet_wrap(~ molecule, scales = "free", ncol = 1) +
  scale_fill_brewer(palette = "Set3")

## ----theme_genes---------------------------------------------------------
ggplot(example_genes, aes(xmin = start, xmax = end, y = molecule, fill = gene)) +
  geom_gene_arrow() +
  facet_wrap(~ molecule, scales = "free", ncol = 1) +
  scale_fill_brewer(palette = "Set3") +
  theme_genes()

## ----make_alignment_dummies----------------------------------------------
dummies <- make_alignment_dummies(
  example_genes,
  aes(xmin = start, xmax = end, y = molecule, id = gene),
  on = "genE"
)

ggplot(example_genes, aes(xmin = start, xmax = end, y = molecule, fill = gene)) +
  geom_gene_arrow() +
  geom_blank(data = dummies) +
  facet_wrap(~ molecule, scales = "free", ncol = 1) +
  scale_fill_brewer(palette = "Set3") +
  theme_genes()

## ----labelled_genes------------------------------------------------------
ggplot(example_genes, aes(xmin = start, xmax = end, y =
                                            molecule, fill = gene, label = gene)) +
  geom_gene_arrow(arrowhead_height = unit(3, "mm"), arrowhead_width = unit(1, "mm")) +
  geom_gene_label(align = "left") +
  geom_blank(data = dummies) +
  facet_wrap(~ molecule, scales = "free", ncol = 1) +
  scale_fill_brewer(palette = "Set3") +
  theme_genes()

## ----reversing_direction, fig.height = 3---------------------------------
example_genes$direction <- ifelse(example_genes$strand == "forward", 1, -1)
ggplot(
  subset(example_genes, molecule == "Genome1"),
  aes(xmin = start, xmax = end, y = strand, fill = gene, forward = direction)
  ) +
  geom_gene_arrow() +
  theme_genes()

## ----subgenes------------------------------------------------------------
ggplot(example_genes, aes(xmin = start, xmax = end, y = molecule)) +
  facet_wrap(~ molecule, scales = "free", ncol = 1) +
  geom_gene_arrow(fill = "white") +
  geom_subgene_arrow(data = example_subgenes,
    aes(xmin = start, xmax = end, y = molecule, fill = gene,
        xsubmin = from, xsubmax = to), color="black", alpha=.7) +
  theme_genes()

## ----subgene labels, fig.height = 2--------------------------------------
ggplot(subset(example_genes, molecule == "Genome4" & gene == "genA"),
       aes(xmin = start, xmax = end, y = strand)
  ) +
  geom_gene_arrow() +
  geom_gene_label(aes(label = gene)) +
  geom_subgene_arrow(
    data = subset(example_subgenes, molecule == "Genome4" & gene == "genA"),
    aes(xsubmin = from, xsubmax = to, fill = subgene)
  ) +
  geom_subgene_label(
    data = subset(example_subgenes, molecule == "Genome4" & gene == "genA"),
    aes(xsubmin = from, xsubmax = to, label = subgene),
    min.size = 0
  )

