plotRmiRtc: Plot object from read.mir or a selected gene and respective...

In RmiR: Package to work with miRNAs and miRNA targets with R

Description

Ploting function for object coming from read.mir or a selected gene and respective miRNAs from a miRtcList object

Usage

  plotRmiRtc(miRtcObj,gene_id=NULL,timeunit="Time",legend.x=NULL,legend.y=NULL,svgTips=FALSE,svgname=NULL,height=10,width=15)

Arguments

miRtcObj	A data.frame resulting from read.mir or RmiR functions or a miRtcList-class object.
gene_id	Selected gene_id contained in a miRtcList-class object.
timeunit	Name for the abscissae axes, normally a time unit like "Hours", "PD" etc.
legend.x	Position of the legend in the x-axes.
legend.y	Position of the legend in the y-axes.
svgTips	TRUE if you want to use the RSVGTipsDevice, default is FALSE.
svgname	Name for the SVG image output.
height	Height of the graphs.
width	Width of the graphs.

Details

The function plots the trends of a gene target with the specified gene_id and respective miRNA contained in a miRtcList-class object.

If the miRtcObj argument is a dataframe coming from read.mir function, the resulting plot will be a point graph in SVG format. Each couple miRNA/Target is a point, the x value is the gene target expression value and the y value is the microRNA expression value. To decrease the size of the graph is possible to select just the desired miRNAs or gene targets in the data.frame

See Also

readRmiRtc,miRtcList

Examples

	
        data(RmiR)
        res1 <- read.mir(genes=gene1, mirna=mir1, annotation="hgug4112a.db")
        res2 <- read.mir(genes=gene2, mirna=mir2, annotation="hgug4112a.db")
        res3 <- read.mir(genes=gene3, mirna=mir3, annotation="hgug4112a.db")

        res_tc <- RmiRtc(timeline=c("res1", "res2", "res3"),
			 timevalue=c(12, 48, 72))
        res <- readRmiRtc(res_tc, correlation=-0.9, exprLev=1,
			  annotation="hgug4112a.db")

	## List of genes with anti-correlated miRNAs:
        
	res$reps

	## Plot of the first gene of the list:
	plotRmiRtc (res, gene_id=351, timeunit="Hours")

	## Setting the position of the legend:
	
	plotRmiRtc (res,gene_id=351, legend.x=50, legend.y=0, timeunit="Hours")

	## Plot with RSVGTipsDevice:
	
	plotRmiRtc (res,gene_id=351, legend.x=50, legend.y=0, timeunit="Hours",
		    svgTips=TRUE)

	## Plot of a read.mir results:
	
	plotRmiRtc (res1, svgname="gene1.svg", svgTips=TRUE)
   

RmiR documentation built on Nov. 8, 2020, 5:17 p.m.