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https://github.com/Farre-lab/syntenyPlotteR

R package to draw syntenic plots in 3 different styles
https://github.com/Farre-lab/syntenyPlotteR

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R package to draw syntenic plots in 3 different styles

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# syntenyPlotteR



R package to draw synteny plots in three different styles



This package has been developed by Joana Damas (),

Sarah Quigley (), Denis Larkin ()

and Marta Farré ()



It has been tested in Windows 10 R v4.0.3, Windows 11 with R v4.1.1 and

v4.2.2 and MAC OS Ventura 13.1



## To install:



### Using CRAN



``` r

install.packages("syntenyPlotteR")

library(syntenyPlotteR)

```



### Using github



``` r

install.packages("devtools")

library(devtools)

devtools::install_github("Farre-lab/syntenyPlotteR")

library(syntenyPlotteR)

```



------------------------------------------------------------------------



## Input files



### Input Alignment file



We provide a function to modify the output of DESCHRAMBLER or any other

synteny tool that creates this type of file:



**Alignment output file format for reformat.syntenyData function**






**Otherwise, you can provide your input Alignment file separated by

tabs**



DO NOT include a header line



- Reference chromosome ID

- Reference start position

- Reference end position

- Target chromosome

- Target start position

- Target end position

- Orientation

- Reference species ID

- Target species ID



**Example input alignment file format for the three functions**






### Chromosome Length file for draw.ideogram and draw.linear functions



Please provide a file containing all aligned species in order from

newest species – top of file – to ancestor – end of file, following this

format, separated by tabs



DO NOT include a header line



- Chromosome ID

- Chromosome length

- Species ID



**Example file format**



## 



------------------------------------------------------------------------



## Reformatting alignment data



The syntenyPlotteR package includes a function to reformat alignment

synteny data such as from DESCHRAMBLER or inferCARs - this does not

curate files only reformats it



The function outputs a text file containing the reformatted alignment

data As default the function saves the file to a temporary directory,

this can be overridden using the `directory` parameter

i.e. `directory = "path/to/directory"`.



### Usage



``` r

library(syntenyPlotteR)



reformat.syntenyData("file_data", "output.filename", reference.species = "reference.sps", target.species = "target.sps")

```



- file_data - alignment output file from DESCHRAMBLER/infeCARs

- output.filename - output file name for reformatted data in a character

  string



There are optional parameters for some customization of this function:



- reference.species - reference species ID as character string for final

  output table

- target.species - target species ID as character string for final

  output table

- directory - directory where to save text file

  i.e. `directory = "path/to/directory"`



### Example code using data files in *inst/extdata/*



``` r

reformat.syntenyData("example_map_1.map", "reformatted.data")

```



------------------------------------------------------------------------



## Evolution Highway style



### Usage



``` r

library(syntenyPlotteR)



draw.eh("output", chrRange, "data_file", fileformat = "png", colour = "lightblue", inverted.colour = "lightpink", w = 5.5, h = 10, ps = 10)

```



- output - String assigned to name of output file name

- chrRange - The range of chromosomes of the reference species this is

  entered as either a single number i.e. 1 or a range of numbers

  i.e. 1:22. *Note: if you are inputting sex chromosomes or chromosomes

  with characters in the name input a concatenated string

  i.e. c(1,2,3,“X”)*

- data_file - File containing the syntenic blocks of alignments of one

  or more target species aligned to a single reference



There are optional parameters for some customization of this function:



- fileformat - format for saving the image i.e. png or pdf, parameter

  use: `fileformat = "pdf"` (the default value is “png”)

- colour - colour of the syntenic blocks (not inverted blocks),

  parameter use: `colour = "red"` (the default value is “lightblue”, see

  Rcolour pallette for colour options)

- inverted.colour - colour of the inverted syntenic blocks, parameter

  use: `inverted.colour = "blue"` (the default value is “lightpink”, see

  Rcolour pallette for colour options)

- w - The width of the image created can be changed by using: `w = 5.5`

  (default)

- h - The height of the image created can be changed by using: `h = 10`

  (default)

- ps - The point size of the image created can be changed by using:

  `ps = 10` (default)

- directory - directory where to save image file

  i.e. `directory = "path/to/directory"` (default is save to temporary

  directory)



**Example code using data files in *inst/extdata/***



``` r

draw.eh("outputName", c(17,"X"), "example_eh_alignments_2.txt", fileformat = "pdf")

```



**Example output**



## 



------------------------------------------------------------------------



## Chromosome painting style



### Usage



``` r

library(syntenyPlotteR)  



draw.ideogram("file_data", "sizefile", "output", fileformat = "png", colours = colours.default, w=8.5, h=10, ps=5)

```



- file_data - file containing the syntenic blocks

- sizefile - tab separated file of all chromosome, scaffold, or contig

  lengths and the species identifier, in order from first target species

  in the alignment files followed by the first reference species in the

  alignment files – top of file – to the last target species and

  reference species in the alignment files – end of file.

- output - string assigned to the output file name



There are optional parameters for some customization of this function:



- fileformat - format for saving the image i.e. png or pdf, parameter

  use: `fileformat = "pdf"` (the default value is “png”)

- colours - colours to assign to the ideograms in a concatenated string

  of chromosome IDs with assigned colour values which can be found with

  R colour Pallette, paramter use:

  `colours = c("1" = "red", "2" = "blue", "3" = "green","4" = "orange", "5" = "purple","X" = "grey")`

  if no colours are assigned default values will be used but colours

  MUST be assigned to all chromosomes

- w - The width of the image created can be changed by using: `w = 5.5`

  (default)

- h - The height of the image created can be changed by using: `h = 10`

  (default)

- ps - The point size of the image created can be changed by using:

  `ps = 10` (default)

- directory - directory where to save image file

  i.e. `directory = "path/to/directory"` (default is save to temporary

  directory)



Target is the species which chromosomes will be painted. Reference will

be used for painting and diagonals. Chromosomes will be in the same

order as in the target sizes file.



**Example code using data files in *inst/extdata/***



``` r

draw.ideogram("example_alignment_1.txt", "example_lengths.txt", "example.ideogram")

```



**Example output**






------------------------------------------------------------------------



## Linear style



### Usage



``` r

library(syntenyPlotteR)



draw.linear(output, sizefile, ..., fileformat = "png", colours = colours.default, w=13, h=5, opacity = .5)

```



- output - string assigned to the output file name

- sizefile - tab separated file of all chromosome, scaffold, or contig

  lengths and the species identifier, in order from first target species

  in the alignment files followed by the first reference species in the

  alignment files – top of file – to the last target species and

  reference species in the alignment files – end of file.

- … - files containing the syntenic blocks (one file per alignment, in

  order from first target/reference (most recent species pairwise

  alignment in ancestral reconstruction data) alignment file to last

  target/reference (ancestor pairwise alignment in ancestral

  reconstruction data) alignment file)



Please ensure any species identifiers used between length and alignment

files are matching (same identifiers and letter case)



There are optional parameters for some customization of this function:



- fileformat - format for saving the image i.e. png or pdf, parameter

  use: `fileformat = "pdf"` (the default value is “png”)

- colours - colours to assign to the bands between ideograms in a

  concatenated string of chromosome IDs with assigned colour values

  which can be found with R colour Pallette, paramter use:

  `colours = c("1" = "red", "2" = "blue", "3" = "green","4" = "orange", "5" = "purple","X" = "grey")`

  if no colours are assigned default values will be used but colours

  MUST be assigned to all chromosomes

- w - The width of the image created can be changed by using: `w = 5.5`

  (default)

- h - The height of the image created can be changed by using: `h = 10`

  (default)

- opacity - the opacity of the ribbons can be changes using inputting:

  `opacity = .5` (default)

- directory - directory where to save image file

  i.e. `directory = "path/to/directory"` (default is save to temporary

  directory)



**Example code using data files in *inst/extdata/***



``` r

draw.linear("example_linear", "example_lengths.txt", "example_alignment_1.txt", "example_alignment_2.txt", "example_alignment_3.txt")

```



**Example output**






------------------------------------------------------------------------



### Citation:



Sarah Quigley, Joana Damas, Denis M Larkin, Marta Farré, syntenyPlotteR: a user-friendly R package to visualize genome synteny, ideal for both experienced and novice bioinformaticians, Bioinformatics Advances, Volume 3, Issue 1, 2023, vbad161, https://doi.org/10.1093/bioadv/vbad161