Nothing
## ---- 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------------------------------------------------------
ggplot(example_genes, aes(xmin = start, xmax = end, y = molecule, fill = gene,
forward = orientation)) +
geom_gene_arrow() +
facet_wrap(~ molecule, scales = "free", ncol = 1) +
scale_fill_brewer(palette = "Set3") +
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
)
## -----------------------------------------------------------------------------
ggplot(example_genes, aes(xmin = start, xmax = end, y = molecule, fill = gene)) +
geom_feature(
data = example_features,
aes(x = position, y = molecule, forward = forward)
) +
geom_feature_label(
data = example_features,
aes(x = position, y = molecule, label = name, forward = forward)
) +
geom_gene_arrow() +
geom_blank(data = example_dummies) +
facet_wrap(~ molecule, scales = "free", ncol = 1) +
scale_fill_brewer(palette = "Set3") +
theme_genes()
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