Circ.lineplot: Circ.lineplot
In dieterich-lab/CircTest: Test circRNA dependence on host genes

Description Usage Arguments Examples

Plot circRNA and host gene expression as line plot. Plot per gene-wise.

Circ.lineplot(Circ, Linear, CircCoordinates = None, plotrow = "1",
  size = 18, ncol = 2, groupindicator1 = NULL, groupindicator2 = NULL,
  x = "Conditions", y = "Counts", circle_description = c(1:3),
  gene_column = None)

`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 'Counts'.
`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.

data(Coordinates)
data(Circ)
data(Linear)
Circ.lineplot(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),x='Ages',circle_description = c(1:3), gene_column = 4 )