Package 'gggenes' reference manual

Title:	Draw Gene Arrow Maps in 'ggplot2'
Description:	A 'ggplot2' extension for drawing gene arrow maps.
Authors:	David Wilkins [aut, cre], Zachary Kurtz [ctb]
Maintainer:	David Wilkins <[email protected]>
License:	GPL-2
Version:	0.5.1.9002
Built:	2025-02-20 05:15:54 UTC
Source:	https://github.com/wilkox/gggenes

A set of example dummy alignment genes.

Description

Dummy genes, similar to those generated with make_alignment_dummies(), for example purposes only.

Usage

example_dummies
example_dummies

Format

A data frame with eight rows and three variables:

molecule: the genome
start: the start position of the dummy
end: the end position of the dummy
gene: the name of the dummy gene

A set of example genetic features.

Description

Genetic features for example purposes only.

Usage

example_features

example_features_polar
example_features

example_features_polar

Format

A data frame with 23 rows and five variables:

molecule: the genome
name: the name of the feature
type: the type of the feature
position: the position of the feature
forward: is the feature oriented, and if so in the forward direction?

An object of class data.frame with 6 rows and 5 columns.

A set of example genes.

Description

Genes for example purposes only.

Usage

example_genes

example_genes_polar

example_subgenes

example_subgenes_polar
example_genes

example_genes_polar

example_subgenes

example_subgenes_polar

Format

A data frame with 72 rows and six variables:

molecule: the genome
gene: the name of the gene
start: the start position of the gene
end: the end position of the gene
strand: the strand of the gene
orientation: the orientation of the gene

example_subgenes (143 rows) also contains:

subgene: the name of the subgene
from: the start position of the subgene segment
to: the end position of the subgene segment

An object of class data.frame with 18 rows and 6 columns.

An object of class data.frame with 143 rows and 9 columns.

An object of class data.frame with 40 rows and 9 columns.

A set of example terminators.

Description

Terminators for example purposes only.

Usage

example_terminators

example_terminators_polar
example_terminators

example_terminators_polar

Format

A data frame with two rows and three variables:

molecule: the genome
name: the name of the terminator
position: the position of the terminator

An object of class data.frame with 2 rows and 3 columns.

A 'ggplot2' geom to draw point genetic features

Description

geom_feature() draws lines to indicate the positions of point genetic features, for example restriction sites, origins of replication or transcription start sites.

Usage

geom_feature(
  mapping = NULL,
  data = NULL,
  stat = "identity",
  position = "identity",
  na.rm = FALSE,
  show.legend = NA,
  inherit.aes = FALSE,
  feature_height = unit(3, "mm"),
  feature_width = unit(3, "mm"),
  arrowhead_width = unit(2, "mm"),
  ...
)
geom_feature(
  mapping = NULL,
  data = NULL,
  stat = "identity",
  position = "identity",
  na.rm = FALSE,
  show.legend = NA,
  inherit.aes = FALSE,
  feature_height = unit(3, "mm"),
  feature_width = unit(3, "mm"),
  arrowhead_width = unit(2, "mm"),
  ...
)

Arguments

`mapping`, `data`, `stat`, `position`, `na.rm`, `show.legend`, `inherit.aes`, `...`	As standard for ggplot2. inherit.aes is set to FALSE by default, as features are not likely to share any plot aesthetics other than y.
`feature_height`	`grid::unit()` object giving the height of a feature above the molecule line. Can be set as a negative value to draw features below the line. Defaults to 3 mm.
`feature_width`	`grid::unit()` object giving the width of a feature (distance from the elbow to the tip of the arrow). Only relevant for oriented features. Defaults to 3 mm.
`arrowhead_width`	`grid::unit()` object giving the width of the arrowhead indicating the direction of an oriented feature. Only relevant for oriented features. Defaults to 2 mm.

Details

Features are drawn as vertical lines extending from the horizontal line representing the molecule. The position of the feature is expressed with the x aesthetic. Optionally, the forward aesthetic can be used to specific an orientation for the feature (e.g. the direction of transcription), in which case an angled arrowhead will be added. The forward aesthetic assumes that the x-axis is oriented in the normal direction, i.e. increasing from left to right; if it is not, the values in forward will need to be inverted manually.

Aesthetics

x (required; position of the feature)
y (required; molecule)
forward (optional; if TRUE, or a value coercible to TRUE, the feature will be drawn with an arrowhead pointing right, if FALSE, pointing left, if NA, the feature will be drawn as a vertical line)
alpha
colour
linetype
linewidth (the former size aesthetic has been deprecated and will be removed in future versions)

Examples


ggplot2::ggplot(example_genes, ggplot2::aes(xmin = start, xmax = end,
                                            y = molecule, fill = gene)) +
  geom_gene_arrow() +
  geom_feature(data = example_features, ggplot2::aes(x = position, y = molecule, 
                                                     forward = forward)) +
  ggplot2::facet_wrap(~ molecule, scales = "free")

ggplot2::ggplot(example_genes, ggplot2::aes(xmin = start, xmax = end,
                                            y = molecule, fill = gene)) +
  geom_gene_arrow() +
  geom_feature(data = example_features, ggplot2::aes(x = position, y = molecule, 
                                                     forward = forward)) +
  ggplot2::facet_wrap(~ molecule, scales = "free")

A 'ggplot2' geom to add text labels to point genetic features

Description

geom_feature_label() adds text labels to features drawn with geom_feature().

Usage

geom_feature_label(
  mapping = NULL,
  data = NULL,
  stat = "identity",
  position = "identity",
  na.rm = FALSE,
  show.legend = FALSE,
  inherit.aes = FALSE,
  feature_height = unit(4, "mm"),
  label_height = unit(3, "mm"),
  ...
)
geom_feature_label(
  mapping = NULL,
  data = NULL,
  stat = "identity",
  position = "identity",
  na.rm = FALSE,
  show.legend = FALSE,
  inherit.aes = FALSE,
  feature_height = unit(4, "mm"),
  label_height = unit(3, "mm"),
  ...
)

Arguments

`mapping`, `data`, `stat`, `position`, `na.rm`, `show.legend`, `inherit.aes`, `...`	As standard for ggplot2. inherit.aes is set to FALSE by default, as features are not likely to share any plot aesthetics other than y.
`feature_height`	`grid::unit()` object giving the height of the feature being labelled, and hence the distance of the label above or below the molecule line. Can be set as a negative value for features drawn below the line. Defaults to 4 mm, to align labels with the default height of `geom_feature()`.
`label_height`	`grid::unit()` object giving the height of the label text. Defaults to 3 mm.

Details

Standard 'ggplot2' aesthetics for text are supported (see Aesthetics).

Aesthetics

x (required; position of the feature)
y (required; molecule)
label (required; the label text)
forward (optional; will draw text in the appropriate location for features with angled arrowheads)
colour
size
alpha
family
fontface
angle

Examples


ggplot2::ggplot(example_genes, ggplot2::aes(xmin = start, xmax = end,
                                            y = molecule, fill = gene)) +
  geom_gene_arrow() +
  geom_feature(data = example_features, ggplot2::aes(x = position, y = molecule, 
                                                     forward = forward)) +
  geom_feature_label(data = example_features,
                     ggplot2::aes(x = position, y = molecule, label = name, 
                                  forward = forward)) + 
  ggplot2::facet_wrap(~ molecule, scales = "free")

ggplot2::ggplot(example_genes, ggplot2::aes(xmin = start, xmax = end,
                                            y = molecule, fill = gene)) +
  geom_gene_arrow() +
  geom_feature(data = example_features, ggplot2::aes(x = position, y = molecule, 
                                                     forward = forward)) +
  geom_feature_label(data = example_features,
                     ggplot2::aes(x = position, y = molecule, label = name, 
                                  forward = forward)) + 
  ggplot2::facet_wrap(~ molecule, scales = "free")

A 'ggplot2' geom to draw genes as arrows

Description

geom_gene_arrow() draws genes as arrows, allowing gene maps to be drawn.

Usage

geom_gene_arrow(
  mapping = NULL,
  data = NULL,
  stat = "identity",
  position = "identity",
  na.rm = FALSE,
  show.legend = NA,
  inherit.aes = TRUE,
  arrowhead_width = grid::unit(4, "mm"),
  arrowhead_height = grid::unit(4, "mm"),
  arrow_body_height = grid::unit(3, "mm"),
  ...
)
geom_gene_arrow(
  mapping = NULL,
  data = NULL,
  stat = "identity",
  position = "identity",
  na.rm = FALSE,
  show.legend = NA,
  inherit.aes = TRUE,
  arrowhead_width = grid::unit(4, "mm"),
  arrowhead_height = grid::unit(4, "mm"),
  arrow_body_height = grid::unit(3, "mm"),
  ...
)

Arguments

`mapping`, `data`, `stat`, `position`, `na.rm`, `show.legend`, `inherit.aes`, `...`	As standard for ggplot2.
`arrowhead_width`	`grid::unit()` object giving the width of the arrowhead. Defaults to 4 mm. If the gene is drawn smaller than this width, only the arrowhead will be drawn, compressed to the length of the gene.
`arrowhead_height`	`grid::unit()` object giving the height of the arrowhead. Defaults to 4 mm.
`arrow_body_height`	`grid::unit()` object giving the height of the body of the arrow. Defaults to 3 mm.

Details

This geom draws genes as arrows along a horizontal line representing the molecule. The start and end locations of the gene are expressed with the xmin and xmax aesthetics, while the molecule can be specified with the y aesthetic. Optionally, an additional forward aesthetic can be used to reverse the orientation of some or all genes from that implied by xmin and xmax.

Unless the plot is faceted with a free x scale, all the molecules will share a common x axis. This means that if the locations are very different across different molecules, the genes might appear very small and squished together with a lot of unnecessary empty space. To get around this, either facet the plot with scales = "free_x", or normalise the gene locations if their exact locations are not important.

See make_alignment_dummies() for a method to align genes between molecules.

Aesthetics

xmin,xmax (start and end of the gene; will be used to determine gene orientation)
y (molecule)
forward (if any value that is not TRUE, or coercible to TRUE, the gene arrow will be drawn in the opposite direction to that determined by xmin and xmax)
alpha
colour
fill
linetype
linewidth (the former size aesthetic has been deprecated and will be removed in future versions)

Examples


ggplot2::ggplot(example_genes, ggplot2::aes(xmin = start, xmax = end,
                                            y = molecule, fill = gene)) +
geom_gene_arrow() +
ggplot2::facet_wrap(~ molecule, scales = "free")

ggplot2::ggplot(example_genes, ggplot2::aes(xmin = start, xmax = end,
                                            y = molecule, fill = gene)) +
geom_gene_arrow() +
ggplot2::facet_wrap(~ molecule, scales = "free")

A 'ggplot2' geom to add text labels to gene arrows

Description

geom_gene_label() can be used to add a text label to genes drawn with geom_gene_arrow().

Usage

geom_gene_label(
  mapping = NULL,
  data = NULL,
  stat = "identity",
  position = "identity",
  na.rm = FALSE,
  show.legend = FALSE,
  inherit.aes = TRUE,
  padding.x = grid::unit(1, "mm"),
  padding.y = grid::unit(0.1, "lines"),
  align = "centre",
  min.size = 4,
  grow = F,
  reflow = F,
  height = grid::unit(3, "mm"),
  ...
)
geom_gene_label(
  mapping = NULL,
  data = NULL,
  stat = "identity",
  position = "identity",
  na.rm = FALSE,
  show.legend = FALSE,
  inherit.aes = TRUE,
  padding.x = grid::unit(1, "mm"),
  padding.y = grid::unit(0.1, "lines"),
  align = "centre",
  min.size = 4,
  grow = F,
  reflow = F,
  height = grid::unit(3, "mm"),
  ...
)

Arguments

`mapping`, `data`, `stat`, `position`, `na.rm`, `show.legend`, `inherit.aes`, `...`	Standard geom arguments as for `ggplot2::geom_text()`.
`padding.x`, `padding.y`	`grid::unit()` object, giving horizontal or vertical padding around the text. Defaults to 1 mm and 0.1 lines respectively.
`align`	Where inside the gene to place the text label. Default is 'centre'; other options are 'left' and 'right'.
`min.size`	Minimum font size, in points. If provided, text that would need to be shrunk below this size to fit inside the gene arrow will not be drawn. Defaults to 4 pt.
`grow`	If `TRUE`, text will be grown as well as shrunk to fill the arrow.
`reflow`	If `TRUE`, text will be reflowed (wrapped) to better fit the arrow.
`height`	`grid::unit()` object giving the maximum height of the text. Defaults to 3 mm, which is the default height of gene arrows drawn with `geom_gene_arrow()`.

Details

geom_gene_label() uses the 'ggfittext' package to fit text to genes. All text drawing options available in ggfittext::geom_fit_text() (growing, reflowing, etc.) are also available here. For full details on how these options work, see the documentation for ggfittext::geom_fit_text().

Standard 'ggplot2' aesthetics for text are supported (see Aesthetics).

Aesthetics

xmin,xmax (start and end of the gene; required)
y (molecule; required)
label (the label text; required)
colour
size
alpha
family
fontface
angle

Examples


ggplot2::ggplot(example_genes, ggplot2::aes(xmin = start, xmax = end,
  y = molecule, fill = gene, label = gene)) +
  geom_gene_arrow() +
  geom_gene_label() +
  ggplot2::facet_wrap(~ molecule, ncol = 1, scales = "free") +
  theme_genes()
ggplot2::ggplot(example_genes, ggplot2::aes(xmin = start, xmax = end,
  y = molecule, fill = gene, label = gene)) +
  geom_gene_arrow() +
  geom_gene_label() +
  ggplot2::facet_wrap(~ molecule, ncol = 1, scales = "free") +
  theme_genes()

A 'ggplot2' geom to draw subgene segments of gene arrows

Description

geom_subgene_arrow() draws subgenes segments within gene arrows drawn with geom_gene_arrow().

Usage

geom_subgene_arrow(
  mapping = NULL,
  data = NULL,
  stat = "identity",
  position = "identity",
  na.rm = FALSE,
  show.legend = NA,
  inherit.aes = TRUE,
  arrowhead_width = grid::unit(4, "mm"),
  arrowhead_height = grid::unit(4, "mm"),
  arrow_body_height = grid::unit(3, "mm"),
  ...
)
geom_subgene_arrow(
  mapping = NULL,
  data = NULL,
  stat = "identity",
  position = "identity",
  na.rm = FALSE,
  show.legend = NA,
  inherit.aes = TRUE,
  arrowhead_width = grid::unit(4, "mm"),
  arrowhead_height = grid::unit(4, "mm"),
  arrow_body_height = grid::unit(3, "mm"),
  ...
)

Arguments

`mapping`, `data`, `stat`, `position`, `na.rm`, `show.legend`, `inherit.aes`, `...`	As standard for 'ggplot2'.
`arrowhead_width`	`grid::unit()` object giving the width of the arrowhead. Defaults to 4 mm. If the gene is drawn smaller than this width, only the arrowhead will be drawn, compressed to the length of the gene.
`arrowhead_height`	`grid::unit()` object giving the height of the arrowhead. Defaults to 4 mm.
`arrow_body_height`	`grid::unit()` object giving the height of the body of the arrow. Defaults to 3 mm.

Details

The start and end locations of the subgene are given with the xsubmin and xsubmax aesthetics. geom_subgene_arrow() requires some information about the 'parent' gene, provided with the same aesthetics used for geom_gene_arrow(): start and end locations of the 'parent' gene with the xmin and xmax aesthetics, the molecule with the y aesthetic, and optionally the direction with the forward aesthetic. If the geometry of the parent gene has been changed with arrowhead_width, arrowhead_height or arrow_body_height, identical parameters should be given to geom_subgene_arrow().

Aesthetics

xmin,xmax (start and end of the gene; will be used to determine gene orientation)
xsubmin,xsubmax (start and end of subgene segment). Should be consistent with xmin/xmax
y (molecule)
forward (if FALSE, or coercible to FALSE, the gene arrow will be drawn in the opposite direction to that determined by xmin and xmax)
alpha
colour
fill
linetype
linewidth (the former size aesthetic has been deprecated and will be removed in future versions)

Examples


ggplot2::ggplot(example_genes, ggplot2::aes(xmin = start, xmax = end,
                                            y = molecule)) +
geom_gene_arrow() +
geom_subgene_arrow(data = example_subgenes,
      ggplot2::aes(xmin = start, xmax = end, xsubmin = from, xsubmax = to,
                   y = molecule, fill = gene)) +
ggplot2::facet_wrap(~ molecule, scales = "free")

ggplot2::ggplot(example_genes, ggplot2::aes(xmin = start, xmax = end,
                                            y = molecule)) +
geom_gene_arrow() +
geom_subgene_arrow(data = example_subgenes,
      ggplot2::aes(xmin = start, xmax = end, xsubmin = from, xsubmax = to,
                   y = molecule, fill = gene)) +
ggplot2::facet_wrap(~ molecule, scales = "free")

A 'ggplot2' geom to add text labels to subgenes

Description

geom_subgene_label() can be used to add a text label to subgenes drawn with geom_subgene_arrow().

Usage

geom_subgene_label(
  mapping = NULL,
  data = NULL,
  stat = "identity",
  position = "identity",
  na.rm = FALSE,
  show.legend = FALSE,
  inherit.aes = TRUE,
  padding.x = grid::unit(1, "mm"),
  padding.y = grid::unit(0.1, "lines"),
  align = "centre",
  min.size = 4,
  grow = F,
  reflow = F,
  height = grid::unit(3, "mm"),
  ...
)
geom_subgene_label(
  mapping = NULL,
  data = NULL,
  stat = "identity",
  position = "identity",
  na.rm = FALSE,
  show.legend = FALSE,
  inherit.aes = TRUE,
  padding.x = grid::unit(1, "mm"),
  padding.y = grid::unit(0.1, "lines"),
  align = "centre",
  min.size = 4,
  grow = F,
  reflow = F,
  height = grid::unit(3, "mm"),
  ...
)

Arguments

`mapping`, `data`, `stat`, `position`, `na.rm`, `show.legend`, `inherit.aes`, `...`	Standard geom arguments as for `ggplot2::geom_text()`.
`padding.x`, `padding.y`	`grid::unit()` object, giving horizontal or vertical padding around the text. Defaults to 1 mm and 0.1 lines respectively.
`align`	Where inside the subgene to place the text label. Default is 'centre'; other options are 'left' and 'right'.
`min.size`	Minimum font size, in points. If provided, text that would need to be shrunk below this size to fit inside the subgene will not be drawn. Defaults to 4 pt.
`grow`	If `TRUE`, text will be grown as well as shrunk to fill the subgene.
`reflow`	If `TRUE`, text will be reflowed (wrapped) to better fit the subgene.
`height`	`grid::unit()` object giving the maximum height of the text. Defaults to 3 mm, which is the default height of gene arrows (and therefore of subgenes) drawn with `geom_gene_arrow()`.

Details

geom_subgene_label() uses the 'ggfittext' package to fit text to genes. All text drawing options available in ggfittext::geom_fit_text() (growing, reflowing, etc.) are also available here. For full details on how these options work, see the documentation for ggfittext::geom_fit_text().

Standard 'ggplot2' aesthetics for text are supported (see Aesthetics.)

Aesthetics

xsubmin,xsubmax (start and end of the subgene; required)
y (molecule; required)
colour
size
alpha
family
fontface
angle

A 'ggplot2' geom to draw transcription terminators

Description

geom_terminator() draws a 'T-shaped' glyph representing the position of a transcription terminator.

Usage

geom_terminator(
  mapping = NULL,
  data = NULL,
  stat = "identity",
  position = "identity",
  na.rm = FALSE,
  show.legend = NA,
  inherit.aes = FALSE,
  terminator_height = unit(3, "mm"),
  terminator_width = unit(3, "mm"),
  ...
)
geom_terminator(
  mapping = NULL,
  data = NULL,
  stat = "identity",
  position = "identity",
  na.rm = FALSE,
  show.legend = NA,
  inherit.aes = FALSE,
  terminator_height = unit(3, "mm"),
  terminator_width = unit(3, "mm"),
  ...
)

Arguments

`mapping`, `data`, `stat`, `position`, `na.rm`, `show.legend`, `inherit.aes`, `...`	As standard for ggplot2. inherit.aes is set to FALSE by default, as terminators are not likely to share any plot aesthetics other than y.
`terminator_height`	`grid::unit()` object giving the height of the vertical 'pillar' of the terminator glyph above the molecule line. Can be set as a negative value to draw terminators below the line. Defaults to 3 mm.
`terminator_width`	`grid::unit()` object giving the width of the horizontal 'beam' of the terminator glyph. Defaults to 3 mm.

Aesthetics

x (required; position of the terminator)
y (required; molecule)
alpha
color
linetype
linewidth (the former size aesthetic has been deprecated and will be removed in future versions)

Examples


ggplot2::ggplot(example_genes, ggplot2::aes(xmin = start, xmax = end,
                                            y = molecule, fill = gene)) +
  geom_gene_arrow() +
  geom_terminator(data = example_terminators, ggplot2::aes(x = position, y = molecule)) +
  ggplot2::facet_wrap(~ molecule, scales = "free")

ggplot2::ggplot(example_genes, ggplot2::aes(xmin = start, xmax = end,
                                            y = molecule, fill = gene)) +
  geom_gene_arrow() +
  geom_terminator(data = example_terminators, ggplot2::aes(x = position, y = molecule)) +
  ggplot2::facet_wrap(~ molecule, scales = "free")

A 'ggplot2' geom to add text labels to transcription terminators

Description

geom_terminator_label() adds text labels to terminators drawn with geom_terminator().

Usage

geom_terminator_label(
  mapping = NULL,
  data = NULL,
  stat = "identity",
  position = "identity",
  na.rm = FALSE,
  show.legend = FALSE,
  inherit.aes = FALSE,
  terminator_height = unit(4, "mm"),
  label_height = unit(3, "mm"),
  ...
)
geom_terminator_label(
  mapping = NULL,
  data = NULL,
  stat = "identity",
  position = "identity",
  na.rm = FALSE,
  show.legend = FALSE,
  inherit.aes = FALSE,
  terminator_height = unit(4, "mm"),
  label_height = unit(3, "mm"),
  ...
)

Arguments

`mapping`, `data`, `stat`, `position`, `na.rm`, `show.legend`, `inherit.aes`, `...`	As standard for ggplot2. inherit.aes is set to FALSE by default, as terminators are not likely to share any plot aesthetics other than y.
`terminator_height`	`grid::unit()` object giving the height of the terminator being labelled, and hence the distance of the label above or below the molecule line. Can be set as a negative value for terminators drawn below the line. Defaults to 4 mm, to align labels with the default height of `geom_terminator()`.
`label_height`	`grid::unit()` object giving the height of the label text. Defaults to 3 mm.

Details

Standard 'ggplot2' aesthetics for text are supported (see Aesthetics).

Aesthetics

x (required; position of the terminator)
y (required; molecule)
label (required; the label text)
colour
size
alpha
family
fontface
angle

Examples


ggplot2::ggplot(example_genes, ggplot2::aes(xmin = start, xmax = end,
                                            y = molecule, fill = gene)) +
  geom_gene_arrow() +
  geom_terminator(data = example_terminators, 
                  ggplot2::aes(x = position, y = molecule)) +
  geom_terminator_label(data = example_terminators,
                     ggplot2::aes(x = position, y = molecule, label = name)) +
  ggplot2::facet_wrap(~ molecule, scales = "free")

ggplot2::ggplot(example_genes, ggplot2::aes(xmin = start, xmax = end,
                                            y = molecule, fill = gene)) +
  geom_gene_arrow() +
  geom_terminator(data = example_terminators, 
                  ggplot2::aes(x = position, y = molecule)) +
  geom_terminator_label(data = example_terminators,
                     ggplot2::aes(x = position, y = molecule, label = name)) +
  ggplot2::facet_wrap(~ molecule, scales = "free")

Prepare dummy data to visually align a single gene across faceted molecules

Description

make_alignment_dummies() helps you to visually align genes across molecules that have been faceted with a free x scale. The output of this function is a data frame of dummy genes. If these dummy genes are added to a 'ggplot2' plot with ggplot::geom_blank(), they will extend the x axis range in such a way that the start or end of a selected gene is visually aligned across the facets.

Usage

make_alignment_dummies(data, mapping, on, side = "left")
make_alignment_dummies(data, mapping, on, side = "left")

Arguments

`data`	Data frame of genes. This is almost certainly the same data frame that will later be passed to `ggplot2::ggplot()`.
`mapping`	Aesthetic mapping, created with `ggplot2::aes()`. Must contain the following aesthetics: `xmin`, `xmax`, `y`, and `id` (a unique identifier for each gene).
`on`	Name of gene to be visually aligned across facets. This gene must be present in 'data', in the column mapped to the `id` aesthetic.
`side`	Should the visual alignment be of the 'left' (default) or 'right' side of the gene?

Examples


dummies <- make_alignment_dummies(example_genes, ggplot2::aes(xmin = start,
  xmax = end, y = molecule, id = gene), on = "genE")

ggplot2::ggplot(example_genes, ggplot2::aes(xmin = start, xmax = end,
    y = molecule, fill = gene)) +
  geom_gene_arrow() +
  ggplot2::geom_blank(data = dummies) +
  ggplot2::facet_wrap(~ molecule, scales = "free", ncol = 1)

dummies <- make_alignment_dummies(example_genes, ggplot2::aes(xmin = start,
  xmax = end, y = molecule, id = gene), on = "genE")

ggplot2::ggplot(example_genes, ggplot2::aes(xmin = start, xmax = end,
    y = molecule, fill = gene)) +
  geom_gene_arrow() +
  ggplot2::geom_blank(data = dummies) +
  ggplot2::facet_wrap(~ molecule, scales = "free", ncol = 1)

A 'ggplot2' theme for drawing gene maps

Description

This theme removes extraneous plot elements for drawing an 'arrows-on-a-string' style gene map in 'ggplot2'.theme_genes_flipped() is like theme_genes(), but for flipped coordinates.

Usage

theme_genes()

theme_genes_flipped()
theme_genes()

theme_genes_flipped()

Details

This theme removes strip text (the text that labels facets when you use ggplot2::facet_wrap() or ggplot::facet_grid()). This makes it easier to draw molecules on different x scales by setting the y aesthetic to the molecule, then faceting with facet_grid( ~ molecule, scales = "free").

Examples


ggplot2::ggplot(example_genes, ggplot2::aes(xmin = start, xmax = end,
                                            y = molecule, fill = gene)) +
geom_gene_arrow() +
ggplot2::facet_wrap(~ molecule, scales = "free") +
theme_genes()

ggplot2::ggplot(example_genes, ggplot2::aes(xmin = start, xmax = end,
                                            y = molecule, fill = gene)) +
geom_gene_arrow() +
ggplot2::facet_wrap(~ molecule, scales = "free") +
theme_genes()

Package 'gggenes'

Help Index

A set of example dummy alignment genes.

Description

Usage

Format

A set of example genetic features.

Description

Usage

Format

A set of example genes.

Description

Usage

Format

A set of example terminators.

Description

Usage

Format

A 'ggplot2' geom to draw point genetic features

Description

Usage

Arguments

Details

Aesthetics

See Also

Examples

A 'ggplot2' geom to add text labels to point genetic features

Description

Usage

Arguments

Details

Aesthetics

See Also

Examples

A 'ggplot2' geom to draw genes as arrows

Description

Usage

Arguments

Details

Aesthetics

See Also

Examples

A 'ggplot2' geom to add text labels to gene arrows

Description

Usage

Arguments

Details

Aesthetics

See Also

Examples

A 'ggplot2' geom to draw subgene segments of gene arrows

Description

Usage

Arguments

Details

Aesthetics

See Also

Examples

A 'ggplot2' geom to add text labels to subgenes

Description

Usage

Arguments

Details

Aesthetics

A 'ggplot2' geom to draw transcription terminators

Description

Usage

Arguments

Aesthetics

See Also

Examples

A 'ggplot2' geom to add text labels to transcription terminators

Description

Usage

Arguments

Details

Aesthetics

See Also

Examples

Prepare dummy data to visually align a single gene across faceted molecules