PlotPlastidGenome: Generate Plasit Genome Plot

In shuyuzheng/Chloroplot: A package to plot Chloroplast genome.

Description

Generate Plasit Genome Plot

Usage

PlotPlastidGenome(
  plot.tables,
  save = TRUE,
  file.type = "pdf",
  text.size = 1,
  height = c(0.1, 0.2, 0.07),
  file.name = NULL,
  shadow = TRUE,
  ir.gc = TRUE,
  gc.per.gene = TRUE,
  pseudo = TRUE,
  legend = TRUE,
  ssc.converse = FALSE,
  lsc.converse = FALSE,
  ira.converse = FALSE,
  irb.converse = FALSE,
  genome.length = TRUE,
  total.gc = TRUE,
  show.indel = TRUE,
  gene.no = TRUE,
  rrn.no = TRUE,
  trn.no = TRUE,
  organelle_type = TRUE,
  background = "grey90",
  gc.color = "grey30",
  gc.background = "grey70",
  info.background = "black",
  ir.color = "#2F3941",
  ssc.color = "#82B6E2",
  lsc.color = "#299E96",
  shadow.color = "#0000FF20",
  psa.color = "#2A6332",
  psb.color = "#4C8805",
  pet.color = "#7F992C",
  atp.color = "#9FBB3D",
  ndh.color = "#FEEE50",
  rbc.color = "#4D9E3F",
  rpo.color = "#AE2D29",
  rsp.color = "#D6AD7C",
  rpl.color = "#9C7A4B",
  clp_mat_inf.color = "#D9662D",
  ycf.color = "#71B8A9",
  trn.color = "#172C7F",
  rrn.color = "#D1382A",
  other_gene.color = "#7D7D7D",
  show.genes = c("psa", "psb", "pet", "atp", "ndh", "rbc", "rpo", "rps", "rpl",
    "clp|mat|inf", "ycf", "trn", "rrn", "OTHER"),
  gene_axis_ir.color = ir.color,
  gene_axis_ssc.color = ssc.color,
  gene_axis_lsc.color = lsc.color,
  cu.bias = TRUE,
  customize.ring1 = NULL,
  customize.ring1.type = "line",
  customize.ring1.color = gc.color,
  customize.ring2 = NULL,
  customize.ring2.type = "line",
  customize.ring2.color = gc.color,
  customize.ring3 = NULL,
  customize.ring3.color = gc.color
)

Arguments

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.
shadow	A logical value. If it is TRUE, the section of IR regions will be highlighted by shadows.
ir.gc	A logical value. If it is TRUE, the gc content for IR, LSC, and SSC regions will be plot with deep colors.
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.
ssc.converse	A logical value. If it is TRUE, the SSC region will be converted to its reverse complementary version
lsc.converse	A logical value. If it is TRUE, the LSC region will be converted to its reverse complementary version
ira.converse	A logical value. If it is TRUE, the IRA region will be converted to its reverse complementary version
irb.converse	A logical value. If it is TRUE, the IRB region will be converted to its reverse complementary version
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.
show.indel	A logical value. If it is TRUE, the SNP, insertion and deletion areas in IR regions will be highlighted on 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.
ir.color	An R color object. It indicates the color for the background of IR sectors.
ssc.color	An R color object. It indicates the color for the background of SSC sectors.
lsc.color	An R color object. It indicates the color for the background of LSC sectors.
shadow.color	An R color object. It indicates the color for the shadow casted from IR sectors.
psa.color	An R color object. It indicates the color for genes of photosystem I
psb.color	An R color object. It indicates the color for genes of photosystem II
pet.color	An R color object. It indicates the color for genes of cytochrome b/f complex
atp.color	An R color object. It indicates the color for genes of ATP synthesis
ndh.color	An R color object. It indicates the color for genes of NADH dehydrogenase
rbc.color	An R color object. It indicates the color for genes of RubisCO larg subunit
rpo.color	An R color object. It indicates the color for genes of RNA polymerase
rsp.color	An R color object. It indicates the color for genes of small ribosomal protein
rpl.color	An R color object. It indicates the color for genes of large ribosomal protein
clp_mat_inf.color	An R color object. It indicates the color for genes of clpP, matK, or infA
ycf.color	An R color object. It indicates the color for genes of hypothetical reading frame
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
gene_axis_ir.color	An R color object. It indicates the color for other genes.
gene_axis_ssc.color	An R color object. It indicates the color for other genes.
gene_axis_lsc.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.type	A charactor. It indicate the plot type in customize.ring1. Avaliable values are "line", "line + filling", "line + dot", "line + dot + filling", "step line", "step line + filling", "vertical line"
customize.ring1.color	An R color object. It indicates the color for the plots in customized ring 1.
customize.ring2	A data frame. It must contain 2 columns: position: 1-base genomic coordinate for the features. value: the values for the features.
customize.ring2.type	A charactor. It indicate the plot type in customize.ring2. Avaliable 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.ring3	A data frame. It must contain 2 columns: start: 1-base genomic coordinate for the start point of the features. end: 1-base genomic 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. A valiable values are "psa","psb","pet","atp", "ndh","rbc", "rpo","rps","rpl", "clp|mat|inf","ycf", "trn","rrn", "OTHER"

Value

A plot for chloroplast genome.

References

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.