Circ.ratioplot: Circ.ratioplot
In biomedscience/hCIRC: biocomputational tools for computational biology

Description Usage Arguments Examples

View source: R/Circ.ratioplot.R

Plot the ratio of circRNAs to the total transcripts (circRNA plus liner RNA).

Circ.ratioplot(
  Circ,
  Linear,
  CircCoordinates = None,
  plotrow = "1",
  size = 24,
  ncol = 2,
  groupindicator1 = NULL,
  groupindicator2 = NULL,
  x = "Conditions",
  y = "circRNA/(circRNA+Linear)",
  lab_legend = "groupindicator1",
  circle_description = c(1:3),
  gene_column = None,
  y_axis_range = 1,
  colour_mode = "colour"
)

`Circ`	CircRNACount file. A file of circRNA read count table. First three columns are circRNA coordinates, and followed by columns for circRNA read counts, each sample per column.
`Linear`	LinearCount file. A file of circRNA host gene expression count table. Same configuration as CircRNACount file.
`CircCoordinates`	BED format circRNA coordinates file.
`plotrow`	The rownumber or rowname in the CircRNACount table corresponding the specific gene which you want to plot.
`size`	the text size. Default 18.
`ncol`	if groupindicator2 is provided, specify the panel layout. Default 2.
`groupindicator1`	A vector of group indicators. For example, ages.
`groupindicator2`	An other vector of group indicators. For example, tissues. This indicator will be used to segement plots out.
`x`	x axis lable. Default 'Conditions'.
`y`	y axis lable. Default 'circRNA/(circRNA+Linear)'.
`lab_legend`	legend title
`circle_description`	Column indices which do not carry circle/linear read counts.
`gene_column`	Column index of the column containing the gene name in CircCoordinates if available, otherwise its chosen from Circ.
`y_axis_range`	Range of the y axis to keep all plots withint he same range

data(Coordinates)
data(Circ)
data(Linear)
data(Coordinates)
data(Circ)
data(Linear)
Circ.ratioplot(Circ,Linear,Coordinates,plotrow=10,groupindicator1=c(rep('1days',6),rep('4days',6),rep('20days',6)),groupindicator2=rep(c(rep('Female',4),rep('Male',2)),3),lab_legend='Ages', circle_description = c(1:3), gene_column = 4, y_axis_range = 1)