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https://github.com/wilkox/gggenes

➡️️➡️️⬅️️➡️️ Draw gene arrow maps in ggplot2
https://github.com/wilkox/gggenes

genetics ggplot2 r

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➡️️➡️️⬅️️➡️️ Draw gene arrow maps in ggplot2

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README 

        
---

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knitr::opts_chunk$set(

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# gggenes



gggenes is a [ggplot2](https://ggplot2.tidyverse.org) extension for drawing

gene arrow maps.



## Installing gggenes



Install the stable version of gggenes from CRAN:



`install.packages("gggenes")`



If you want the development version, install it from GitHub:



`devtools::install_github("wilkox/gggenes")`



## Drawing gene arrows with `geom_gene_arrow()`



`geom_gene_arrow()` is a ggplot2 geom that represents genes with arrows. The

start and end locations of the genes within their molecule(s) are mapped to the

`xmin` and `xmax` aesthetics respectively. These start and end locations are

used to determine the directions in which the arrows point. The `y` aesthetic

must be mapped to the molecule(s). If you are drawing more than one molecule,

and the numerical locations of the genes are not similar across molecules, you

almost certainly want to facet the plot with `scales = "free"` to avoid drawing

ridiculously large molecules with ridiculously tiny genes.



```{r geom_gene_arrow}

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")

```



## Beautifying the plot with `theme_genes`



Because the resulting plot can look cluttered, a ggplot2 theme `theme_genes`

is provided with some sensible defaults.



```{r 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()

```



## Aligning genes across facets with `make_alignment_dummies()`



Often you will want a certain gene to be vertically aligned across the faceted

molecules. `make_alignment_dummies()` generates a set of dummy genes that if

added to the plot with `geom_blank()` will extend the range of each facet to

visually align the selected gene across facets.



```{r 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()

```



## Labelling genes with `geom_gene_label()`



To label individual genes, provide a `label` aesthetic and use

`geom_gene_label()`. `geom_gene_label()` uses the

[ggfittext](https://github.com/wilkox/ggfittext) package to fit the label text

inside the gene arrows; see the ggfittext documentation for more details on how

it resizes and reflows text to make it fit.



```{r 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 gene direction with the optional `forward` aesthetic



By default, genes arrows are drawn pointing in the direction implied by `xmin`

and `xmax`. You can override this with the optional `forward` aesthetic, which

can be useful when the gene coordinates and orientation are encoded as separate

variables.



If `forward` is TRUE (the default), or any value that coerces to TRUE such as

1, the gene will be drawn pointing in the implied direction, i.e. from `xmin`

to `xmax`. If `forward` is FALSE, or any value that coerces to FALSE such as

0, the gene will be drawn in the reverse of this implied direction:



```{r 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()

```



## Viewing subgene segments



We can highlight subgene segments, such as protein domains or local alignments,

using `geom_subgene_arrow()`.



This works similarly to `geom_gene_arrow()`, but in addition to `xmin` and

`xmax` (which determine the gene boundaries), we need the aesthetics `xsubmin`

and `xsubmax` to determine the subgene boundaries. `geom_gene_arrow()` will

produce pretty arrowheads, as long as `xmin >= xsubmin` and `xmax >= xsubmax`

for all subgenes (subgenes that break gene boundaries will be skipped with a

warning).



The suggested usage is to use `geom_gene_arrow()` with no fill, and then add a

subgene layer over this:



```{r 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()

```



To label subgenes, we can use `geom_subgene_label()`, which works similarly to

`geom_gene_label()` with the major difference that it requires `xsubmin` and

`xsubmax` aesthetics (not `xmin` and `xmax`).



```{r 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

  )

```



## Drawing point genetic features



We can draw point genetic features, such as restriction sites or transcription

start sites, with `geom_feature()`, and label them with `geom_feature_label()`.

Both of these geoms take an optional `forward` aesthetic to indicate whether a

feature is oriented and, if so, in what direction (`TRUE` meaning oriented

towards the right and `FALSE` meaning towards the left).



```{r}

ggplot(example_genes, aes(xmin = start, xmax = end, y = molecule, fill = gene, label = 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_gene_label() +

  geom_blank(data = example_dummies) +

  facet_wrap(~ molecule, scales = "free", ncol = 1) +

  scale_fill_brewer(palette = "Set3") +

  theme_genes()

```



We can draw and label transcription terminators with `geom_terminator()` and

`geom_terminator_label()`.



```{r}

ggplot(example_genes, aes(xmin = start, xmax = end, y = molecule, fill = gene, label = 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_terminator(data = example_terminators, aes(x = position, y = molecule)) +

  geom_terminator_label(data = example_terminators, 

                        aes(x = position, y = molecule, label = name)) +

  geom_gene_arrow() +

  geom_gene_label() +

  geom_blank(data = example_dummies) +

  facet_wrap(~ molecule, scales = "free", ncol = 1) +

  scale_fill_brewer(palette = "Set3") +

  theme_genes()

```



## Experimental: drawing in polar coordinates



The current development version introduces drawing in polar coordinates, by

adding `coord_polar()` to the plot. This works with all gene, subgene, feature,

and terminator geoms.



```{r}

ggplot(example_genes_polar, aes(xmin = start, xmax = end, y = molecule, fill = gene, label = gene)) +

  geom_feature(

    data = example_features_polar,

    aes(x = position, y = molecule, forward = forward)

  ) +

  geom_feature_label(

    data = example_features_polar,

    aes(x = position, y = molecule, label = name, forward = forward)

  ) +

  geom_terminator(data = example_terminators_polar, aes(x = position, y = molecule)) +

  geom_terminator_label(data = example_terminators_polar, 

                        aes(x = position, y = molecule, label = name)) +

  geom_gene_arrow() +

  geom_gene_label() +

  scale_fill_brewer(palette = "Set3") +

  coord_polar() +

  scale_y_discrete(limits = c("", "Genome6", "Genome1"))

```



## Other genetic features



Do you have an idea, suggestion or request for another type of feature for

gggenes to draw? [Open a new issue](https://github.com/wilkox/gggenes/issues/new) 

and it will be considered.



## Related packages



- [gggenomes](https://thackl.github.io/gggenomes/) for visualising comparative genomics

- [plasmapR](https://github.com/BradyAJohnston/plasmapR) for quickly drawing plasmid maps from GenBank files