PlotMitGenome: Generate Mitochondrion Genome Plot
In shuyuzheng/Chloroplot: A package to plot Chloroplast genome.

Description Usage Arguments Value References

View source: R/plot_genome.R

Generate Mitochondrion Genome Plot

PlotMitGenome(
  plot.tables,
  save = TRUE,
  file.type = "pdf",
  text.size = 1,
  height = c(0.1, 0.2, 0.07),
  file.name = NULL,
  gc.per.gene = TRUE,
  pseudo = TRUE,
  legend = TRUE,
  genome.length = TRUE,
  total.gc = TRUE,
  gene.no = TRUE,
  rrn.no = TRUE,
  trn.no = TRUE,
  organelle_type = TRUE,
  background = "grey90",
  gc.color = "grey30",
  gc.background = "grey70",
  info.background = "black",
  nad.color = "#2A6332",
  sdh.color = "#4C8805",
  cob.color = "#7F992C",
  cox.color = "#FEEE50",
  atp.color = "#9FBB3D",
  ccmF.color = "#4D9E3F",
  mmt.color = "#AE2D29",
  rps.color = "#D6AD7C",
  rpl.color = "#9C7A4B",
  mat.color = "#D9662D",
  orf.color = "#71B8A9",
  trn.color = "#172C7F",
  rrn.color = "#D1382A",
  other_gene.color = "#7D7D7D",
  show.genes = c("nad|nd", "sdh", "cob", "cox|cytb", "atp", "ccmF", "mtt", "rps",
    "rpl", "mat", "orf", "trn", "rrn", "OTHER"),
  cu.bias = TRUE,
  customize.ring1 = NULL,
  customize.ring1.color = "grey30",
  customize.ring1.type = "line",
  customize.ring2.color = "grey30",
  customize.ring2 = NULL,
  customize.ring2.type = "line",
  customize.ring3 = NULL,
  customize.ring3.color = "grey30"
)

`plot.tables`	a list contains information of IR region, gene, and gc count of the genome. It can be generated by function `PlotTab`.
`save`	A logical value. If it is `TRUE`, the plot will be saved in work directory.
`file.type`	A charactor. It indicates the format of the file in which the plot will be saved. Options are: "pdf", "png", "jpeg","bmp", "tiff". By default, it is set as "pdf".
`text.size`	A numeric value. It indicates the size of all texts in the plot. For exmple, `text.size = 1.5` means all the texts in the plot will be enlarged as 1.5 times of their original size.
`height`	A vector of numeric value. The elements of it indicat the height of gene layer, GC count layer and IR region layer, respectively. Default setting is "0.1, 0.2, 0.07". The taltal circle plot region always has a radius of 1, so a height of 0.1 means 10% of the circle radius.
`file.name`	A charactor. It indicates the name of the file in which the plot will be saved. By default, it is set as the specie's name.
`gc.per.gene`	A logical value. If it is `TRUE`, the GC content of each gene will be show by a darker part in gene rectangles.
`pseudo`	A logical value. If it is `TRUE`, the pseudo genes (if there is some in the species) will be marked with a "*" at the end of the labels.
`legend`	A logical value. If it is `TRUE`, the legend for gene colors will be shown.
`genome.length`	A logical value. If it is `TRUE`, the length of genome will be shown in the center of the plot.
`total.gc`	A logical value. If it is `TRUE`, the GC content of whole genome will be shown in the center of the plot.
`gene.no`	A logical value. If it is `TRUE`, the number of genes in the genome will be shown in the center of the plot.
`rrn.no`	A logical value. If it is `TRUE`, the number of rRNAs in the genome will be shown in the center of the plot.
`trn.no`	A logical value. If it is `TRUE`, the number of tRNAs in the genome will be shown in the center of the plot.
`background`	An R color object. It indicates the color for the background of entire plot area.
`gc.color`	An R color object. It indicates the color for the lines in gc count plot.
`gc.background`	An R color object. It indicates the color for the background of gc count plot area.
`info.background`	An R color object. It indicates the color for the background of central area where species' information was shown.
`nad.color`	An R color string. It indicates the color for genes of complex I (NADH dehydrogenase)
`sdh.color`	An R color string. It indicates the color for genes of complex II (succinate dehydrogenase)
`cob.color`	An R color string. It indicates the color for genes of complex III (ubichinol cytochrome reductase)
`cox.color`	An R color string. It indicates the color for genes of complex IV (cytochrome c oxidase)
`atp.color`	An R color string. It indicates the color for genes of ATP synthase
`ccmF.color`	An R color string. It indicates the color for genes of cytochrome c biogenesi
`mmt.color`	An R color string. It indicates the color for genes of transport membrane protein
`rps.color`	An R color string. It indicates the color for genes of ribosomal proteins (SSU)
`rpl.color`	An R color string. It indicates the color for genes of ribosomal proteins (LSU)
`mat.color`	An R color string. It indicates the color for genes of maturases
`orf.color`	An R color string. It indicates the color for ORFs
`trn.color`	An R color object. It indicates the color for genes of transfer RNA
`rrn.color`	An R color object. It indicates the color for genes of ribosomal RNA
`other_gene.color`	An R color object. It indicates the color for other genes
`cu.bias`	A logical value. If it is `TRUE`, the condon usage bias metric for each gene will be shown in the labels. The metric “Measure Independent of Length and Composition (MILC)” was used for evaluate the bias. You can find more details in the reference paper.
`customize.ring1`	A data frame. It must contain 2 columns: position: 1-base genomic coordinate for the features. value: the values for the features.
`customize.ring1.color`	An R color object. It indicates the color for the plots in customized ring 1.
`customize.ring1.type`	A character. It indicate the plot type in customize.ring1. Available values are "line", "line + filling", "line + dot", "line + dot + filling", "step line", "step line + filling", "vertical line"
`customize.ring2.color`	An R color object. It indicates the color for the plots in customized ring 2.
`customize.ring2`	A data frame. It must contain 2 columns: position: 1-base genome coordinate for the features. value: the values for the features.
`customize.ring2.type`	A character. It indicate the plot type in customize.ring2. Available values are "line", "line + filling", "line + dot", "line + dot + filling", "step line", "step line + filling", "vertical line"
`customize.ring3`	A data frame. It must contain 2 columns: start: 1-base genome coordinate for the start point of the features. end: 1-base genome coordinate for the end point of the features. value: the values for the features.
`customize.ring3.color`	An R color object. It indicates the color for the plots in customized ring 3.
`organelle`	A logical value. If it is `TRUE`, the organelle type of the genome will be shown in the center of the plot.
`show.gene`	A vector of characters. It indicates which classes of genes will be shown on the plot. Avaliable values are "nad\|nd","sdh","cob", "cox\|cytb","atp", "ccmF","mtt","rps","rpl", "mat","orf","trn","rrn", "OTHER"

A plot for chloroplast genome.

Supek, Fran, and Kristian Vlahovicek. “Comparison of codon usage measures and their applicability in prediction of microbial gene expressivity.” BMC bioinformatics vol. 6 182. 19 Jul. 2005, doi:10.1186/1471-2105-6-182

shuyuzheng/Chloroplot documentation built on Dec. 23, 2021, 1:28 a.m.