plot.R
In allogamous/EnvRtype: Envirotyping Tools for Crop Research and Genetic Improvment
# plot 1: enviromental variables panel
require(ggplot2)
require(EnvRtype)
names.window <- c('1-intial growing','2-leaf expansion I','3-leaf expansion II','4-flowering','5-grain filling','6-maturation')
time.window <- c(0,15,35,65,90,120)
out=EnvTyping(env.data = df.clim,env.id = 'env',var.id='T2M',by.interval = T,time.window = time.window, names.window = names.window)
# plot 1
ggplot() +
scale_x_discrete(expand = c(0,0))+
scale_y_discrete(expand = c(0,0))+
scale_fill_gradientn(colours= rainbow(15))+
geom_tile(data=out,aes(x=reorder(env,Freq), y=reorder(env.variable,Freq),fill=Freq))+
ylab('Envirotype ID\n')+
xlab("\nEnvironment ID")+
labs(fill='Frequency')+
theme(axis.title = element_text(size=19),
legend.text = element_text(size=9),
strip.text.y = element_text(size=13,angle=360),
legend.title = element_text(size=17),
strip.background = element_rect(fill="gray95",size=1),
legend.position = 'bottom')
# plot 2: distribution of envirotypes
out=EnvTyping(env.data = df.clim,env.id = 'env',var.id='VPD',by.interval = T,time.window = time.window, names.window = names.window)
require(reshape2)
out=data.frame(out,colsplit(out$env.variable,pattern = '_',names = c('var2','freq','stages')))
ggplot() +
#theme_void()+
scale_x_discrete(expand = c(0,0))+
scale_y_continuous(expand = c(0,0))+
# theme_pubclean()+
#scale_fill_manual(values=c('red2','orange2','green3','blue3','violet'))+
facet_grid(var~interval)+ coord_flip()+
geom_bar(data=out, aes(y=Freq, x=env,fill=freq),
position = "fill",stat = "identity",width = 1,size=.2)+
# scale_y_continuous(labels = scales::percent,expand = c(0,0))+ #coord_flip()+
ylab('Absolute Frequency\n of Occurence\n')+
xlab("\nEnvironment ID")+
labs(fill='Envirotype')+
theme(axis.title = element_text(size=19),
# axis.text = element_blank(),
legend.text = element_text(size=9),
strip.text = element_text(size=17),
legend.title = element_text(size=17),
strip.background = element_rect(fill="gray95",size=1),
legend.position = 'bottom')
out=EnvTyping(env.data = df.clim,env.id = 'env',var.id='T2M',by.interval = T,time.window = time.window, names.window = names.window)
require(reshape2)
out=data.frame(out,colsplit(out$env.variable,pattern = '_',names = c('var2','freq','stages')))
ggplot() +
#theme_void()+
scale_x_discrete(expand = c(0,0))+
scale_y_continuous(expand = c(0,0))+
# theme_pubclean()+
#scale_fill_manual(values=c('red2','orange2','green3','blue3','violet'))+
facet_grid(var~interval)+ coord_flip()+
geom_bar(data=out, aes(y=Freq, x=env,fill=freq),
position = "fill",stat = "identity",width = 1,size=.2)+
# scale_y_continuous(labels = scales::percent,expand = c(0,0))+ #coord_flip()+
ylab('Absolute Frequency\n of Occurence\n')+
xlab("\nEnvironment ID")+
labs(fill='Envirotype')+
theme(axis.title = element_text(size=19),
# axis.text = element_blank(),
legend.text = element_text(size=9),
strip.text = element_text(size=17),
legend.title = element_text(size=17),
strip.background = element_rect(fill="gray95",size=1),
legend.position = 'bottom')
out=EnvTyping(env.data = df.clim,env.id = 'env',var.id='SRAD',by.interval = T,time.window = time.window, names.window = names.window)
require(reshape2)
out=data.frame(out,colsplit(out$env.variable,pattern = '_',names = c('var2','freq','stages')))
ggplot() +
#theme_void()+
scale_x_discrete(expand = c(0,0))+
scale_y_continuous(expand = c(0,0))+
# theme_pubclean()+
#scale_fill_manual(values=c('red2','orange2','green3','blue3','violet'))+
facet_grid(var~interval)+ coord_flip()+
geom_bar(data=out, aes(y=Freq, x=env,fill=freq),
position = "fill",stat = "identity",width = 1,size=.2)+
# scale_y_continuous(labels = scales::percent,expand = c(0,0))+ #coord_flip()+
ylab('Absolute Frequency\n of Occurence\n')+
xlab("\nEnvironment ID")+
labs(fill='Envirotype')+
theme(axis.title = element_text(size=19),
# axis.text = element_blank(),
legend.text = element_text(size=9),
strip.text = element_text(size=17),
legend.title = element_text(size=17),
strip.background = element_rect(fill="gray95",size=1),
legend.position = 'bottom')
## another suggestion
ggplot() +
#theme_void()+
scale_x_discrete(expand = c(0,0))+
scale_y_continuous(expand = c(0,0))+
# theme_pubclean()+
#scale_fill_manual(values=c('red2','orange2','green3','blue3','violet'))+
#facet_grid(var~interval)+
coord_flip()+
geom_bar(data=out, aes(y=Freq, x=env,fill=env.variable),
position = "fill",stat = "identity",width = 1,size=.2)+
# scale_y_continuous(labels = scales::percent,expand = c(0,0))+ #coord_flip()+
ylab('Absolute Frequency\n of Occurence\n')+
xlab("\nEnvironment ID")+
labs(fill='Envirotype')+
theme(axis.title = element_text(size=19),
# axis.text = element_blank(),
legend.text = element_text(size=9),
strip.text = element_text(size=17),
legend.title = element_text(size=17),
strip.background = element_rect(fill="gray95",size=1),
legend.position = 'bottom')
# plot 3: distribution of envirotypes per environment
out=EnvTyping(env.data = df.clim,env.id = 'env',var.id='VPD',by.interval = T,time.window = time.window, names.window = names.window)
require(reshape2)
out=data.frame(out,colsplit(out$env.variable,pattern = '_',names = c('var2','freq','stages')))
ggplot() +
#theme_void()+
scale_x_discrete(expand = c(0,0))+
scale_y_continuous(expand = c(0,0))+
# theme_pubclean()+
#scale_fill_manual(values=c('red2','orange2','green3','blue3','violet'))+
facet_grid(~env)+ #coord_flip()+
geom_bar(data=out, aes(y=Freq, x=interval,fill=freq),
position = "fill",stat = "identity",width = 1,size=.2)+
# scale_y_continuous(labels = scales::percent,expand = c(0,0))+ #coord_flip()+
ylab('Absolute Frequency\n of Occurence\n')+
xlab("\nEnvironment ID")+
labs(fill='Envirotype')+
theme(axis.title = element_text(size=19),
axis.text.x = element_text(hjust=1,angle=45),
legend.text = element_text(size=9),
strip.text = element_text(size=17),
legend.title = element_text(size=17),
strip.background = element_rect(fill="gray95",size=1),
legend.position = 'bottom')
out=EnvTyping(env.data = df.clim,env.id = 'env',var.id='T2M',by.interval = T,time.window = time.window, names.window = names.window)
require(reshape2)
out=data.frame(out,colsplit(out$env.variable,pattern = '_',names = c('var2','freq','stages')))
ggplot() +
#theme_void()+
scale_x_discrete(expand = c(0,0))+
scale_y_continuous(expand = c(0,0))+
# theme_pubclean()+
#scale_fill_manual(values=c('red2','orange2','green3','blue3','violet'))+
facet_grid(~env)+ #coord_flip()+
geom_bar(data=out, aes(y=Freq, x=interval,fill=freq),
position = "fill",stat = "identity",width = 1,size=.2)+
# scale_y_continuous(labels = scales::percent,expand = c(0,0))+ #coord_flip()+
ylab('Absolute Frequency\n of Occurence\n')+
xlab("\nEnvironment ID")+
labs(fill='Envirotype')+
theme(axis.title = element_text(size=19),
axis.text.x = element_text(hjust=1,angle=45),
legend.text = element_text(size=9),
strip.text = element_text(size=17),
legend.title = element_text(size=17),
strip.background = element_rect(fill="gray95",size=1),
legend.position = 'bottom')
out=EnvTyping(env.data = df.clim,env.id = 'env',var.id='SRAD',by.interval = T,time.window = time.window, names.window = names.window)
require(reshape2)
out=data.frame(out,colsplit(out$env.variable,pattern = '_',names = c('var2','freq','stages')))
ggplot() +
#theme_void()+
scale_x_discrete(expand = c(0,0))+
scale_y_continuous(expand = c(0,0))+
# theme_pubclean()+
#scale_fill_manual(values=c('red2','orange2','green3','blue3','violet'))+
facet_grid(~env)+ #coord_flip()+
geom_bar(data=out, aes(y=Freq, x=interval,fill=freq),
position = "fill",stat = "identity",width = 1,size=.2)+
# scale_y_continuous(labels = scales::percent,expand = c(0,0))+ #coord_flip()+
ylab('Absolute Frequency\n of Occurence\n')+
xlab("\nEnvironment ID")+
labs(fill='Envirotype')+
theme(axis.title = element_text(size=19),
axis.text.x = element_text(hjust=1,angle=45),
legend.text = element_text(size=9),
strip.text = element_text(size=17),
legend.title = element_text(size=17),
strip.background = element_rect(fill="gray95",size=1),
legend.position = 'bottom')
allogamous/EnvRtype documentation built on Nov. 1, 2024, 3:48 a.m.
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# plot 1: enviromental variables panel
require(ggplot2)
require(EnvRtype)
names.window <- c('1-intial growing','2-leaf expansion I','3-leaf expansion II','4-flowering','5-grain filling','6-maturation')
time.window <- c(0,15,35,65,90,120)
out=EnvTyping(env.data = df.clim,env.id = 'env',var.id='T2M',by.interval = T,time.window = time.window, names.window = names.window)
# plot 1
ggplot() +
scale_x_discrete(expand = c(0,0))+
scale_y_discrete(expand = c(0,0))+
scale_fill_gradientn(colours= rainbow(15))+
geom_tile(data=out,aes(x=reorder(env,Freq), y=reorder(env.variable,Freq),fill=Freq))+
ylab('Envirotype ID\n')+
xlab("\nEnvironment ID")+
labs(fill='Frequency')+
theme(axis.title = element_text(size=19),
legend.text = element_text(size=9),
strip.text.y = element_text(size=13,angle=360),
legend.title = element_text(size=17),
strip.background = element_rect(fill="gray95",size=1),
legend.position = 'bottom')
# plot 2: distribution of envirotypes
out=EnvTyping(env.data = df.clim,env.id = 'env',var.id='VPD',by.interval = T,time.window = time.window, names.window = names.window)
require(reshape2)
out=data.frame(out,colsplit(out$env.variable,pattern = '_',names = c('var2','freq','stages')))
ggplot() +
#theme_void()+
scale_x_discrete(expand = c(0,0))+
scale_y_continuous(expand = c(0,0))+
# theme_pubclean()+
#scale_fill_manual(values=c('red2','orange2','green3','blue3','violet'))+
facet_grid(var~interval)+ coord_flip()+
geom_bar(data=out, aes(y=Freq, x=env,fill=freq),
position = "fill",stat = "identity",width = 1,size=.2)+
# scale_y_continuous(labels = scales::percent,expand = c(0,0))+ #coord_flip()+
ylab('Absolute Frequency\n of Occurence\n')+
xlab("\nEnvironment ID")+
labs(fill='Envirotype')+
theme(axis.title = element_text(size=19),
# axis.text = element_blank(),
legend.text = element_text(size=9),
strip.text = element_text(size=17),
legend.title = element_text(size=17),
strip.background = element_rect(fill="gray95",size=1),
legend.position = 'bottom')
out=EnvTyping(env.data = df.clim,env.id = 'env',var.id='T2M',by.interval = T,time.window = time.window, names.window = names.window)
require(reshape2)
out=data.frame(out,colsplit(out$env.variable,pattern = '_',names = c('var2','freq','stages')))
ggplot() +
#theme_void()+
scale_x_discrete(expand = c(0,0))+
scale_y_continuous(expand = c(0,0))+
# theme_pubclean()+
#scale_fill_manual(values=c('red2','orange2','green3','blue3','violet'))+
facet_grid(var~interval)+ coord_flip()+
geom_bar(data=out, aes(y=Freq, x=env,fill=freq),
position = "fill",stat = "identity",width = 1,size=.2)+
# scale_y_continuous(labels = scales::percent,expand = c(0,0))+ #coord_flip()+
ylab('Absolute Frequency\n of Occurence\n')+
xlab("\nEnvironment ID")+
labs(fill='Envirotype')+
theme(axis.title = element_text(size=19),
# axis.text = element_blank(),
legend.text = element_text(size=9),
strip.text = element_text(size=17),
legend.title = element_text(size=17),
strip.background = element_rect(fill="gray95",size=1),
legend.position = 'bottom')
out=EnvTyping(env.data = df.clim,env.id = 'env',var.id='SRAD',by.interval = T,time.window = time.window, names.window = names.window)
require(reshape2)
out=data.frame(out,colsplit(out$env.variable,pattern = '_',names = c('var2','freq','stages')))
ggplot() +
#theme_void()+
scale_x_discrete(expand = c(0,0))+
scale_y_continuous(expand = c(0,0))+
# theme_pubclean()+
#scale_fill_manual(values=c('red2','orange2','green3','blue3','violet'))+
facet_grid(var~interval)+ coord_flip()+
geom_bar(data=out, aes(y=Freq, x=env,fill=freq),
position = "fill",stat = "identity",width = 1,size=.2)+
# scale_y_continuous(labels = scales::percent,expand = c(0,0))+ #coord_flip()+
ylab('Absolute Frequency\n of Occurence\n')+
xlab("\nEnvironment ID")+
labs(fill='Envirotype')+
theme(axis.title = element_text(size=19),
# axis.text = element_blank(),
legend.text = element_text(size=9),
strip.text = element_text(size=17),
legend.title = element_text(size=17),
strip.background = element_rect(fill="gray95",size=1),
legend.position = 'bottom')
## another suggestion
ggplot() +
#theme_void()+
scale_x_discrete(expand = c(0,0))+
scale_y_continuous(expand = c(0,0))+
# theme_pubclean()+
#scale_fill_manual(values=c('red2','orange2','green3','blue3','violet'))+
#facet_grid(var~interval)+
coord_flip()+
geom_bar(data=out, aes(y=Freq, x=env,fill=env.variable),
position = "fill",stat = "identity",width = 1,size=.2)+
# scale_y_continuous(labels = scales::percent,expand = c(0,0))+ #coord_flip()+
ylab('Absolute Frequency\n of Occurence\n')+
xlab("\nEnvironment ID")+
labs(fill='Envirotype')+
theme(axis.title = element_text(size=19),
# axis.text = element_blank(),
legend.text = element_text(size=9),
strip.text = element_text(size=17),
legend.title = element_text(size=17),
strip.background = element_rect(fill="gray95",size=1),
legend.position = 'bottom')
# plot 3: distribution of envirotypes per environment
out=EnvTyping(env.data = df.clim,env.id = 'env',var.id='VPD',by.interval = T,time.window = time.window, names.window = names.window)
require(reshape2)
out=data.frame(out,colsplit(out$env.variable,pattern = '_',names = c('var2','freq','stages')))
ggplot() +
#theme_void()+
scale_x_discrete(expand = c(0,0))+
scale_y_continuous(expand = c(0,0))+
# theme_pubclean()+
#scale_fill_manual(values=c('red2','orange2','green3','blue3','violet'))+
facet_grid(~env)+ #coord_flip()+
geom_bar(data=out, aes(y=Freq, x=interval,fill=freq),
position = "fill",stat = "identity",width = 1,size=.2)+
# scale_y_continuous(labels = scales::percent,expand = c(0,0))+ #coord_flip()+
ylab('Absolute Frequency\n of Occurence\n')+
xlab("\nEnvironment ID")+
labs(fill='Envirotype')+
theme(axis.title = element_text(size=19),
axis.text.x = element_text(hjust=1,angle=45),
legend.text = element_text(size=9),
strip.text = element_text(size=17),
legend.title = element_text(size=17),
strip.background = element_rect(fill="gray95",size=1),
legend.position = 'bottom')
out=EnvTyping(env.data = df.clim,env.id = 'env',var.id='T2M',by.interval = T,time.window = time.window, names.window = names.window)
require(reshape2)
out=data.frame(out,colsplit(out$env.variable,pattern = '_',names = c('var2','freq','stages')))
ggplot() +
#theme_void()+
scale_x_discrete(expand = c(0,0))+
scale_y_continuous(expand = c(0,0))+
# theme_pubclean()+
#scale_fill_manual(values=c('red2','orange2','green3','blue3','violet'))+
facet_grid(~env)+ #coord_flip()+
geom_bar(data=out, aes(y=Freq, x=interval,fill=freq),
position = "fill",stat = "identity",width = 1,size=.2)+
# scale_y_continuous(labels = scales::percent,expand = c(0,0))+ #coord_flip()+
ylab('Absolute Frequency\n of Occurence\n')+
xlab("\nEnvironment ID")+
labs(fill='Envirotype')+
theme(axis.title = element_text(size=19),
axis.text.x = element_text(hjust=1,angle=45),
legend.text = element_text(size=9),
strip.text = element_text(size=17),
legend.title = element_text(size=17),
strip.background = element_rect(fill="gray95",size=1),
legend.position = 'bottom')
out=EnvTyping(env.data = df.clim,env.id = 'env',var.id='SRAD',by.interval = T,time.window = time.window, names.window = names.window)
require(reshape2)
out=data.frame(out,colsplit(out$env.variable,pattern = '_',names = c('var2','freq','stages')))
ggplot() +
#theme_void()+
scale_x_discrete(expand = c(0,0))+
scale_y_continuous(expand = c(0,0))+
# theme_pubclean()+
#scale_fill_manual(values=c('red2','orange2','green3','blue3','violet'))+
facet_grid(~env)+ #coord_flip()+
geom_bar(data=out, aes(y=Freq, x=interval,fill=freq),
position = "fill",stat = "identity",width = 1,size=.2)+
# scale_y_continuous(labels = scales::percent,expand = c(0,0))+ #coord_flip()+
ylab('Absolute Frequency\n of Occurence\n')+
xlab("\nEnvironment ID")+
labs(fill='Envirotype')+
theme(axis.title = element_text(size=19),
axis.text.x = element_text(hjust=1,angle=45),
legend.text = element_text(size=9),
strip.text = element_text(size=17),
legend.title = element_text(size=17),
strip.background = element_rect(fill="gray95",size=1),
legend.position = 'bottom')
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