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italicizing species names in figures
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@gregbritten
gregbritten committed Nov 10, 2021
1 parent 7be2379 commit 68c9a58
Showing 1 changed file with 62 additions and 59 deletions.
121 changes: 62 additions & 59 deletions greg/gradients.r
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Expand Up @@ -68,11 +68,11 @@ xxx2_h <- ucynb_Ccell_h*xx2_l
xxx3_h <- ucyna_Ccell_h*xx3_l
xxx4_h <- t_Ccell_h*xx4_l

par(mfrow=c(1,1))
plot(-999,ylim=c(1E-3,1E9),log='y',xlim=c(0,20))
lines(dd$LATITUDE,x1+x2+x3+x4)
lines(dd$LATITUDE,xx1+xx2+xx3+xx4)
lines(dd$LATITUDE,xxx1+xxx2+xxx3+xxx4)
# par(mfrow=c(1,1))
# plot(-999,ylim=c(1E-3,1E9),log='y',xlim=c(0,20))
# lines(dd$LATITUDE,x1+x2+x3+x4)
# lines(dd$LATITUDE,xx1+xx2+xx3+xx4)
# lines(dd$LATITUDE,xxx1+xxx2+xxx3+xxx4)


sumnif <- x1+x2+x3+x4
Expand All @@ -87,9 +87,9 @@ sumbio <- xxx1+xxx2+xxx3+xxx4
#
# areaplot(x,y)

pdf('~/dropbox/working/diazotrophs/plots/diazotroph_gradients_10_14_2021.pdf',height=6,width=10)
pdf('~/dropbox/working/diazotrophs/plots/diazotroph_gradients_11_09_2021.pdf',height=6,width=10)
#par(mfrow=c(2,3),mar=c(2,2,2,2),oma=c(2,2,2,5),xpd=TRUE)
par(mfrow=c(2,2),mar=c(2,2,2,2),oma=c(3,3,3,5),xpd=TRUE,family = 'Arial')
par(mfrow=c(2,2),mar=c(2,2,2,2),oma=c(3,3,3,5),xpd=TRUE)
plot(-999,ylim=c(1E-3,1E6),log='y',xlim=c(0,20),las=1,ylab='')
#lines(dd$lat,xx1_h+xx2_h+xx3_h+xx4_h,lwd=2)
lines(dd$lat,(1/r_nifcell_h)*(dd$richelia+1),col='orange',lty=1)
Expand All @@ -99,7 +99,7 @@ par(mfrow=c(2,2),mar=c(2,2,2,2),oma=c(3,3,3,5),xpd=TRUE,family = 'Arial')
mtext(side=2,expression('Cells [cells/m'^2*']'),line=3.5)
# legend('topleft',legend=c('Total','Richelia','UCYN A','UCYN B','Trichodesmium'),lty=c(1,2,2,2,2),lwd=c(2,1,1,1,1),
# col=c('black','orange','blue','red','dark green'),bty='n',cex=0.7)
legend('topleft',legend=c('Richelia','UCYN A','UCYN B','Trichodesmium'),lty=1,lwd=1,
legend('topleft',legend=c(expression(italic('Richelia')),'UCYN-A','UCYN-B',expression(italic('Trichodesmium'))),lty=1,lwd=1,
col=c('orange','blue','red','dark green'),bty='n',cex=0.7)
mtext(adj=0,'a)')

Expand Down Expand Up @@ -132,58 +132,61 @@ par(mfrow=c(2,2),mar=c(2,2,2,2),oma=c(3,3,3,5),xpd=TRUE,family = 'Arial')
dev.off()


###########################################################################
##--GRADIENT PLOT AS PROPORTIONS--#########################################
###########################################################################

pdf('~/dropbox/working/diazotrophs/plots/diazotroph_gradients_05_28_2021.pdf',height=6,width=10)
#par(mfrow=c(2,3),mar=c(2,2,2,2),oma=c(2,2,2,5),xpd=TRUE)
par(mfrow=c(2,2),mar=c(2,2,2,2),oma=c(3,3,3,5),xpd=TRUE)

tot <- xx1_h+xx2_h+xx3_h+xx4_h
#plot(-999,ylim=c(1E-3,1E6),log='y',xlim=c(0,20),las=1,ylab='')
plot(-999,ylim=c(0,100),xlim=c(0,20),las=1,ylab='')
#lines(dd$lat,xx1_h+xx2_h+xx3_h+xx4_h,lwd=2)
lines(dd$lat,(1/r_nifcell_h)*(dd$richelia+1)/tot*100,col='orange',lty=2)
lines(dd$lat,(1/ucynb_nifcell_h)*(dd$ucyn_b+1)/tot*100,col='red',lty=2)
lines(dd$lat,(1/ucyna_nifcell_h)*(dd$ucyn_a+1)/tot*100,col='blue',lty=2)
lines(dd$lat,(1/t_nifcell_h)*(dd$trichodesmium+1)/tot*100,col='dark green',lty=2)
#mtext(side=2,expression('Cells [cells/m'^2*']'),line=3.5)
mtext(side=2,expression('Proportion of Cells'),line=3.5)
legend('topleft',legend=c('Total','Richelia','UCYN A','UCYN B','Trichodesmium'),lty=c(1,2,2,2,2),lwd=c(2,1,1,1,1),
col=c('black','orange','blue','red','dark green'),bty='n',cex=0.7)
mtext(adj=0,'a)')

tot <- xx1_l+xx2_l+xx3_l+xx4_l
#plot(-999,ylim=c(1E-3,1E6),log='y',xlim=c(0,20),las=1,ylab='')
plot(-999,ylim=c(0,100),xlim=c(0,20),las=1,ylab='')
#lines(dd$lat,xx1_l+xx2_l+xx3_l+xx4_l,lwd=2)
lines(dd$lat,(1/r_nifcell_l)*(dd$richelia+1)/tot*100,col='orange',lty=2)
lines(dd$lat,(1/ucynb_nifcell_l)*(dd$ucyn_b+1)/tot*100,col='red',lty=2)
lines(dd$lat,(1/ucyna_nifcell_l)*(dd$ucyn_a+1)/tot*100,col='blue',lty=2)
lines(dd$lat,(1/t_nifcell_l)*(dd$trichodesmium+1)/tot*100,col='dark green',lty=2)
mtext(adj=0,'b)')

tot <- xxx1_l+xxx2_l+xxx3_l+xxx4_l
#plot(-999,ylim=c(1E-13,1E-3),log='y',xlim=c(0,20),las=1,ylab='')
plot(-999,ylim=c(0,100),xlim=c(0,20),las=1,ylab='')
#lines(dd$lat,xxx1_l+xxx2_l+xxx3_l+xxx4_l,lwd=2)
lines(dd$lat,(1/r_nifcell_h)*(r_Ccell_l)*(dd$richelia+1)/tot*100,col='orange',lty=2)
lines(dd$lat,(1/ucynb_nifcell_h)*(ucynb_Ccell_l)*(dd$ucyn_b+1)/tot*100,col='red',lty=2)
lines(dd$lat,(1/ucyna_nifcell_h)*(ucyna_Ccell_l)*(dd$ucyn_a+1)/tot*100,col='blue',lty=2)
lines(dd$lat,(1/t_nifcell_h)*(t_Ccell_l)*(dd$trichodesmium+1)/tot*100,col='dark green',lty=2)
mtext(side=2,expression('Carbon [mmol/m'^2*']'),line=3.5)
mtext(adj=0,'c)')

tot <- xxx1_h+xxx2_h+xxx3_h+xxx4_h
#plot(-999,ylim=c(1E-13,1E-3),log='y',xlim=c(0,20),las=1,ylab='')
plot(-999,ylim=c(0,100),xlim=c(0,20),las=1,ylab='')
#lines(dd$lat,xxx1_h+xxx2_h+xxx3_h+xxx4_h,lwd=2)
lines(dd$lat,(1/r_nifcell_l)*(r_Ccell_h)*(dd$richelia+1)/tot*100,col='orange',lty=2)
lines(dd$lat,(1/ucynb_nifcell_l)*(ucynb_Ccell_h)*(dd$ucyn_b+1)/tot*100,col='red',lty=2)
lines(dd$lat,(1/ucyna_nifcell_l)*(ucyna_Ccell_h)*(dd$ucyn_a+1)/tot*100,col='blue',lty=2)
lines(dd$lat,(1/t_nifcell_l)*(t_Ccell_h)*(dd$trichodesmium+1)/tot*100,col='dark green',lty=2)
mtext(side=1,outer=TRUE,expression('Latitude ('*degree*'N)'),line=0.5)
mtext(adj=0,'d)')

dev.off()
# pdf('~/dropbox/working/diazotrophs/plots/diazotroph_gradients_05_28_2021.pdf',height=6,width=10)
# #par(mfrow=c(2,3),mar=c(2,2,2,2),oma=c(2,2,2,5),xpd=TRUE)
# par(mfrow=c(2,2),mar=c(2,2,2,2),oma=c(3,3,3,5),xpd=TRUE)
#
# tot <- xx1_h+xx2_h+xx3_h+xx4_h
# #plot(-999,ylim=c(1E-3,1E6),log='y',xlim=c(0,20),las=1,ylab='')
# plot(-999,ylim=c(0,100),xlim=c(0,20),las=1,ylab='')
# #lines(dd$lat,xx1_h+xx2_h+xx3_h+xx4_h,lwd=2)
# lines(dd$lat,(1/r_nifcell_h)*(dd$richelia+1)/tot*100,col='orange',lty=2)
# lines(dd$lat,(1/ucynb_nifcell_h)*(dd$ucyn_b+1)/tot*100,col='red',lty=2)
# lines(dd$lat,(1/ucyna_nifcell_h)*(dd$ucyn_a+1)/tot*100,col='blue',lty=2)
# lines(dd$lat,(1/t_nifcell_h)*(dd$trichodesmium+1)/tot*100,col='dark green',lty=2)
# #mtext(side=2,expression('Cells [cells/m'^2*']'),line=3.5)
# mtext(side=2,expression('Proportion of Cells'),line=3.5)
# legend('topleft',legend=c('Total','Richelia','UCYN A','UCYN B','Trichodesmium'),lty=c(1,2,2,2,2),lwd=c(2,1,1,1,1),
# col=c('black','orange','blue','red','dark green'),bty='n',cex=0.7)
# mtext(adj=0,'a)')
#
# tot <- xx1_l+xx2_l+xx3_l+xx4_l
# #plot(-999,ylim=c(1E-3,1E6),log='y',xlim=c(0,20),las=1,ylab='')
# plot(-999,ylim=c(0,100),xlim=c(0,20),las=1,ylab='')
# #lines(dd$lat,xx1_l+xx2_l+xx3_l+xx4_l,lwd=2)
# lines(dd$lat,(1/r_nifcell_l)*(dd$richelia+1)/tot*100,col='orange',lty=2)
# lines(dd$lat,(1/ucynb_nifcell_l)*(dd$ucyn_b+1)/tot*100,col='red',lty=2)
# lines(dd$lat,(1/ucyna_nifcell_l)*(dd$ucyn_a+1)/tot*100,col='blue',lty=2)
# lines(dd$lat,(1/t_nifcell_l)*(dd$trichodesmium+1)/tot*100,col='dark green',lty=2)
# mtext(adj=0,'b)')
#
# tot <- xxx1_l+xxx2_l+xxx3_l+xxx4_l
# #plot(-999,ylim=c(1E-13,1E-3),log='y',xlim=c(0,20),las=1,ylab='')
# plot(-999,ylim=c(0,100),xlim=c(0,20),las=1,ylab='')
# #lines(dd$lat,xxx1_l+xxx2_l+xxx3_l+xxx4_l,lwd=2)
# lines(dd$lat,(1/r_nifcell_h)*(r_Ccell_l)*(dd$richelia+1)/tot*100,col='orange',lty=2)
# lines(dd$lat,(1/ucynb_nifcell_h)*(ucynb_Ccell_l)*(dd$ucyn_b+1)/tot*100,col='red',lty=2)
# lines(dd$lat,(1/ucyna_nifcell_h)*(ucyna_Ccell_l)*(dd$ucyn_a+1)/tot*100,col='blue',lty=2)
# lines(dd$lat,(1/t_nifcell_h)*(t_Ccell_l)*(dd$trichodesmium+1)/tot*100,col='dark green',lty=2)
# mtext(side=2,expression('Carbon [mmol/m'^2*']'),line=3.5)
# mtext(adj=0,'c)')
#
# tot <- xxx1_h+xxx2_h+xxx3_h+xxx4_h
# #plot(-999,ylim=c(1E-13,1E-3),log='y',xlim=c(0,20),las=1,ylab='')
# plot(-999,ylim=c(0,100),xlim=c(0,20),las=1,ylab='')
# #lines(dd$lat,xxx1_h+xxx2_h+xxx3_h+xxx4_h,lwd=2)
# lines(dd$lat,(1/r_nifcell_l)*(r_Ccell_h)*(dd$richelia+1)/tot*100,col='orange',lty=2)
# lines(dd$lat,(1/ucynb_nifcell_l)*(ucynb_Ccell_h)*(dd$ucyn_b+1)/tot*100,col='red',lty=2)
# lines(dd$lat,(1/ucyna_nifcell_l)*(ucyna_Ccell_h)*(dd$ucyn_a+1)/tot*100,col='blue',lty=2)
# lines(dd$lat,(1/t_nifcell_l)*(t_Ccell_h)*(dd$trichodesmium+1)/tot*100,col='dark green',lty=2)
# mtext(side=1,outer=TRUE,expression('Latitude ('*degree*'N)'),line=0.5)
# mtext(adj=0,'d)')
#
# dev.off()



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