############################################################################
# LICENSE INFO:                                                            #
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#    This file is part of CAMPARI.                                         #
#                                                                          #
#    Version 5.0                                                           #
#                                                                          #
#    Copyright (C) 2024, The CAMPARI development team (current and former  #
#                        contributors)                                     #
#                        Andreas Vitalis, Adam Steffen, Rohit Pappu, Hoang #
#                        Tran, Albert Mao, Xiaoling Wang, Jose Pulido,     #
#                        Nicholas Lyle, Nicolas Bloechliger, Marco Bacci,  #
#                        Davide Garolini, Jiri Vymetal, Cassiano Langini,  #
#                        Alessia Del Panta, Francesco Cocina, Julian       #
#                        Widmer                                            #
#                                                                          #
#    Website: http://sourceforge.net/projects/campari/                     #
#                                                                          #
#    CAMPARI is free software: you can redistribute it and/or modify       #
#    it under the terms of the GNU General Public License as published by  #
#    the Free Software Foundation, either version 3 of the License, or     #
#    (at your option) any later version.                                   #
#                                                                          #
#    CAMPARI is distributed in the hope that it will be useful,            #
#    but WITHOUT ANY WARRANTY; without even the implied warranty of        #
#    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the         #
#    GNU General Public License for more details.                          #
#                                                                          #
#    You should have received a copy of the GNU General Public License     #
#    along with CAMPARI.  If not, see <http://www.gnu.org/licenses/>.      #
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# AUTHORSHIP INFO:                                                         #
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#                                                                          #
# MAIN AUTHOR:   Andreas Vitalis                                           #
#                                                                          #
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# load the data
dat <- read.table("CONTACTMAP.dat",skip=1)

cmap <- array(0.0,dim(dat))
for (i in 1:(dim(dat)[1])) {cmap[i,(1:i)] <- as.double(dat[i,(1:i)]); }

dev.new(width=15,height=7.5);
layout(matrix(1:2,nrow=1,ncol=2),widths=c(7.5,7.5),heights=7.5)
image(axes=FALSE,cmap,x=1:(dim(dat)[1]),y=1:(dim(dat)[1]),zlim=c(0,1),col=heat.colors(500)[seq(from=500,to=100,by=-1)],xlab='',ylab='',main='Linear scale')

box()
axis(side=1,tcl=-0.1,at=1:(dim(dat)[2]),labels=array("",c(dim(dat)[2])))
axis(side=2,tcl=-0.1,at=1:(dim(dat)[2]),labels=array("",c(dim(dat)[2])))

axis(side=1,tcl=0.,at=c(1,4,8,13.5,23.5),labels=c('EAM','HLY','AMP','K+','CL-'),cex.axis=1.2,padj=-1.)
axis(side=2,tcl=0.,at=c(1,4,8,13.5,23.5),labels=c('EAM','HLY','AMP','K+','CL-'),cex.axis=1.2,padj=1.2)

arrows(x0=c(-1,-1,-1,-1),x1=c(100,100,100,100),y0=c(1.5,6.5,8.5,18.5),y1=c(1.5,6.5,8.5,18.5),lty=3)
arrows(y0=c(-1,-1,-1,-1),y1=c(100,100,100,100),x0=c(1.5,6.5,8.5,18.5),x1=c(1.5,6.5,8.5,18.5),lty=3)

legend(x=1,y=(dim(dat)[2]),legend=c("0.00","0.25","0.50","0.75","1.00"),fill=heat.colors(500)[c(500,400,300,200,100)],bg='white')

low_value = min(cmap[which(cmap > 0.0)])
image(axes=FALSE,log10(pmax(cmap,10^floor(log10(low_value)))),x=1:(dim(dat)[1]),y=1:(dim(dat)[1]),zlim=c(log10(low_value),0.0),col=heat.colors(abs(floor(log10(low_value)))*100+100)[seq(from=abs(floor(log10(low_value)))*100+100,to=100,by=-1)],xlab='',ylab='',main='Logarithmic scale')

box()
axis(side=1,tcl=-0.1,at=1:(dim(dat)[2]),labels=array("",c(dim(dat)[2])))
axis(side=2,tcl=-0.1,at=1:(dim(dat)[2]),labels=array("",c(dim(dat)[2])))

axis(side=1,tcl=0.,at=c(1,4,8,13.5,23.5),labels=c('EAM','HLY','AMP','K+','CL-'),cex.axis=1.2,padj=-1.)
axis(side=2,tcl=0.,at=c(1,4,8,13.5,23.5),labels=c('EAM','HLY','AMP','K+','CL-'),cex.axis=1.2,padj=1.2)

arrows(x0=c(-1,-1,-1,-1),x1=c(100,100,100,100),y0=c(1.5,6.5,8.5,18.5),y1=c(1.5,6.5,8.5,18.5),lty=3)
arrows(y0=c(-1,-1,-1,-1),y1=c(100,100,100,100),x0=c(1.5,6.5,8.5,18.5),x1=c(1.5,6.5,8.5,18.5),lty=3)

minil = floor(log10(low_value))
legend(x=1,y=(dim(dat)[2]),legend=sprintf("10^-%d",seq(abs(floor(log10(low_value))),0,-1)),fill=heat.colors(abs(floor(log10(low_value)))*100+100)[seq(abs(floor(log10(low_value)))*100+100,100,-100)],bg='white')