R/plotRadiusVS.R

In sahildshah1/gene-surrounder: GeneSurrounder

#' Plot results of GeneSurrounder 
#'
#' \code{plotRadiusVS} plots the results of GeneSurrounder using the output of the geneNIDG function
#
#' @param geneNIDG.gene A dataframe that is the output of the geneNIDG function
#' 


plotRadiusVS <- function(geneNIDG.gene){

geneNIDG.hsa4171 <- geneNIDG.gene

par(mfcol=c(4,1),mar=c(1,4,2,1), oma=c(2,2,2,2),cex.axis = 1.5)


plot(geneNIDG.hsa4171$radius,
-log10(geneNIDG.hsa4171$p.Sphere),
type = 'b',
cex = 2,
pch = 21,
lwd = 2,
bg = 'lightblue',
xlab = '',
ylab = '-log10(p.Sphere)',
ylim = c(0,5),
main = 'MCM2 (DNA replication factor) identified as "mechanistic driver" ',
xaxt='n')

abline(h = -log10(0.01),lty=3,lwd=2)
abline(h = -log10(0.05),lty=4,lwd=2)

# http://seananderson.ca/2013/10/21/panel-letters.html

mtext("(A)", 
	  side = 3, 
	  adj = 0.05, 
	  line = -2.25,
      cex = 1)

# axis(4)
# mtext("(A)", side=4, line=3)


# radius vs p.Decay -------------------------------------------------------

plot(geneNIDG.hsa4171$radius,
-log10(geneNIDG.hsa4171$p.Decay),
type = 'b',
cex = 2,
pch = 21,
lwd = 2,
bg = 'lightblue',
xlab = '',
ylab = '-log10(p.Decay)',
ylim = c(0,5),
xaxt='n')


abline(h = -log10(0.01),lty=3,lwd=2)
abline(h = -log10(0.05),lty=4,lwd=2)

# http://seananderson.ca/2013/10/21/panel-letters.html

mtext("(B)", 
	  side = 3, 
	  adj = 0.05, 
	  line = -2.25,
      cex = 1)



# radius vs p.Fisher -------------------------------------------------------

plot(geneNIDG.hsa4171$radius,
-log10(geneNIDG.hsa4171$p.Fisher),
type = 'b',
cex = 2,
pch = 21,
lwd = 2,
bg = 'lightblue',
xlab = '',
ylab = '-log10(p.NIDG)',
# ylim = c(0,5),
xaxt='n')


abline(h = -log10(0.01),lty=3,lwd=2)
abline(h = -log10(0.05),lty=4,lwd=2)

# http://seananderson.ca/2013/10/21/panel-letters.html

mtext("(C)", 
	  side = 3, 
	  adj = 0.05, 
	  line = -2.25,
      cex = 1)


# radius vs size      -------------------------------------------------------


plot(geneNIDG.hsa4171$radius,
 geneNIDG.hsa4171$size,
type = 'b',
cex = 2,
pch = 21,
bg = 'lightblue',
xlab = 'Neighborhood Radius',
ylab = 'Number of Assayed Genes',
lwd = 2)


abline(h=2708)

# http://seananderson.ca/2013/10/21/panel-letters.html


mtext("(D)", 
	  side = 3, 
	  adj = 0.05, 
	  line = -2.25,
      cex = 1)


}