exec/Figure3_Root_by_depth.R
In bmcnellis/SDEF.analysis: Data Analysis for 2016 San Dimas Experimental Forest Project
### Visualize root data : Figure 4
library(ggplot2)
library(gridExtra)
library(cowplot)
setwd("D:/R_Workspace/SDEF/SDEF.analysis/data")
load('SDEF_roots_post_aggregation_by_month.rda')
### Root length figures
biodensity <- SDEF_roots_post_aggregation_by_month
biodensity[is.na(biodensity)] <- 0
biodensity$se_length <- ((biodensity$sd_length)/sqrt(biodensity$n_length))
biodensity$minse <- abs((biodensity$mean_length -biodensity$se_length))
biodensity$maxse <- (biodensity$mean_length +biodensity$se_length)
#subset by month for graphing
Dec <- subset(biodensity, biodensity$month == "Dec")
Jan <- subset(biodensity, biodensity$month == "Jan")
Feb <- subset(biodensity, biodensity$month == "Feb")
Mar <- subset(biodensity, biodensity$month == "Mar")
May <- subset(biodensity, biodensity$month == "May")
##############
addec <- subset(Dec, Dec$site == 'adenostoma')
gdec <- subset(Dec, Dec$site == 'grass')
p1 <- ggplot(data = addec, aes(y = depth_bin, x = mean_length)) +
scale_y_continuous(trans = "reverse", breaks = unique(biodensity$depth_bin), labels=c("0-10", "10-20", "20-30", "30-40")) +
scale_x_continuous(position = "top", limits = c(0, 9)) + xlab("")+
geom_point(data = addec, aes(colour = "black", size =1), show.legend = F ) +
geom_errorbarh(data=addec, aes(y = depth_bin, x = mean_length, xmin=minse, xmax=maxse, height = .2))
p1 <- p1 + geom_point(data = gdec, aes(colour = "gray", size =1), show.legend = F ,position = position_nudge(y =0.2)) +
geom_errorbarh(data=gdec, position = position_nudge(y =0.2), aes(y = depth_bin, x = mean_length, xmin=minse, xmax=maxse, height = 0.2, color = "gray"))+
scale_color_manual(values = c("black", "gray"), labels(NULL), guides(fill=FALSE))+ theme_bw()+ ylab("Depth (cm)") +
theme(axis.title.y=element_blank(),
axis.text.y=element_blank(),
axis.ticks.y=element_blank())
p1 <- add_sub(p1, "Dec", x = 4.5, hjust = 0)
p1
adjan <- subset(Jan, Jan$site == 'adenostoma')
gjan <- subset(Jan, Jan$site == 'grass')
p2 <- ggplot(data = adjan, aes(y = depth_bin, x = mean_length)) +
scale_y_continuous(trans = "reverse", breaks = unique(biodensity$depth_bin), labels=c("0-10", "10-20", "20-30", "30-40"))+
scale_x_continuous(position = "top", limits = c(0,9))+ xlab("")+
geom_point(data = adjan, aes(colour = "black", size =1), show.legend = F ) +
geom_errorbarh(data=adjan, aes(y = depth_bin, x = mean_length, xmin=minse, xmax=maxse, height = .2))
p2 <- p2 + geom_point(data = gjan, aes(colour = "gray", size =1), show.legend = F , position = position_nudge(y =0.2)) +
geom_errorbarh(data=gjan, position = position_nudge(y =0.2), aes(y = depth_bin, x = mean_length, xmin=minse, xmax=maxse, height = 0.2, color = "gray"))+
theme_bw()+
scale_color_manual(values = c("black", "gray"), labels(NULL), guides(fill=FALSE))+ ylab("")+
theme(axis.title.y=element_blank(),
axis.text.y=element_blank(),
axis.ticks.y=element_blank())
p2 <- add_sub(p2, "Jan", x = 4.5, hjust = 0)
p2
adfeb <- subset(Feb, Feb$site == 'adenostoma')
gfeb <- subset(Feb, Feb$site == 'grass')
p3 <- ggplot(data = adfeb, aes(y = depth_bin, x = mean_length))+
scale_y_continuous(trans = "reverse", breaks = unique(biodensity$depth_bin)) +
scale_x_continuous(position = "top", limits = c(0,9))+ xlab(expression(paste("Mean root length (mm)"))) +
geom_point(data = adfeb, aes(colour = "black", size =1), show.legend = F ) +
geom_errorbarh(data=adfeb, aes(y = depth_bin, x = mean_length, xmin=minse, xmax=maxse, height = .2))
p3 <- p3 + geom_point(data = gfeb, aes(colour = "gray", size =1), show.legend = F , position = position_nudge(y =0.2)) +
geom_errorbarh(data=gfeb, position = position_nudge(y =0.2), aes(y = depth_bin, x = mean_length, xmin=minse, xmax=maxse, height = 0.2, color = "gray"))+
theme_bw()+ scale_color_manual(values = c("black", "gray"), labels(NULL), guides(fill=FALSE))+ ylab("") +
theme(axis.title.y=element_blank(),
axis.text.y=element_blank(),
axis.ticks.y=element_blank(),
axis.title.x.top = element_text(margin = margin(t = 0, r = 20, b = 0, l = 0)))
p3 <- add_sub(p3, "Feb", x = 4.5, hjust = 0)
p3
admar <- subset(Mar, Mar$site == 'adenostoma')
gmar <- subset(Mar, Mar$site == 'grass')
p4<- ggplot(data = admar, aes(y = depth_bin, x = mean_length)) +
scale_y_continuous(trans = "reverse", breaks = unique(biodensity$depth_bin), labels=c("0-10", "10-20", "20-30", "30-40"))+
scale_x_continuous(position = "top", limits = c(0, 9))+
geom_point(data = admar, aes(colour = "black", size =1), show.legend = F ) +
geom_errorbarh(data=admar, aes(y = depth_bin, x = mean_length, xmin=minse, xmax=maxse, height = .2))
p4 <- p4 + geom_point(data = gmar, aes(colour = "gray", size =1), show.legend = F , position = position_nudge(y =0.2)) +
geom_errorbarh(data=gmar, position = position_nudge(y =0.2), aes(y = depth_bin, x = mean_length, xmin=minse, xmax=maxse, height = 0.2, color = "gray"))+
theme_bw()+ylab("")+ xlab("")+
scale_color_manual(values = c("black", "gray"), labels(NULL), guides(fill=FALSE))+ ylab("") +
theme(axis.title.y=element_blank(),
axis.text.y=element_blank(),
axis.ticks.y=element_blank())
p4 <- add_sub(p4, "Mar", x = 4.5, hjust = 0)
p4
admay <- subset(May, May$site == 'adenostoma')
gmay <- subset(May, May$site == 'grass')
p5<- ggplot(data = admay, aes(y = depth_bin, x = mean_length)) +
scale_y_continuous(trans = "reverse", breaks = unique(biodensity$depth_bin), labels=c("0-10", "10-20", "20-30", "30-40"))+
scale_x_continuous(position = "top", limits = c(0, 9))+
geom_point(data = admay, aes(colour = "black", size =1), show.legend = F ) +
geom_errorbarh(data=admay, aes(y = depth_bin, x = mean_length, xmin=minse, xmax=maxse, height = .2))
p5 <- p5 + geom_point(data = gmay, aes(colour = "gray", size =1), show.legend = F, position = position_nudge(y =0.2)) +
geom_errorbarh(data=gmay, position = position_nudge(y =0.2), aes(y = depth_bin, x = mean_length, xmin=minse, xmax=maxse, height = 0.2, color = "gray"))+
theme_bw()+ylab("")+ scale_color_manual(values = c("black", "gray"), labels(NULL), guides(fill=FALSE))+
xlab("")+
theme(axis.title.y=element_blank(),
axis.text.y=element_blank(),
axis.ticks.y=element_blank())
p5 <- add_sub(p5, "May", x = 4.5, hjust = 0)
grid.arrange(p1, p2, p3, p4, p5, ncol=5)
######## Root biomass figures
biodensity$mean_biodensity_dm <- biodensity$mean_biodensity*1000
biodensity$sd_biodensity_dm <- biodensity$sd_biodensity*1000
biodensity[is.na(biodensity)] <- 0
biodensity$se_biodensity_dm <- ((biodensity$sd_biodensity_dm)/sqrt(biodensity$n_biodensity))
biodensity$minse <- abs((biodensity$mean_biodensity_dm -biodensity$se_biodensity_dm))
biodensity$maxse <- (biodensity$mean_biodensity_dm +biodensity$se_biodensity_dm)
Dec <- subset(biodensity, biodensity$month == "Dec")
Jan <- subset(biodensity, biodensity$month == "Jan")
Feb <- subset(biodensity, biodensity$month == "Feb")
Mar <- subset(biodensity, biodensity$month == "Mar")
May <- subset(biodensity, biodensity$month == "May")
##############
addec <- subset(Dec, Dec$site == 'adenostoma')
gdec <- subset(Dec, Dec$site == 'grass')
p1 <- ggplot(data = addec, aes(y = depth_bin, x = mean_biodensity_dm)) +
scale_y_continuous(trans = "reverse", breaks = unique(biodensity$depth_bin), labels=c("0-10", "10-20", "20-30", "30-40")) +
scale_x_continuous(position = "top", limits = c(0, .35)) + xlab("")+
geom_point(data = addec, aes(colour = "black", size =1), show.legend = F ) +
geom_errorbarh(data=addec, aes(y = depth_bin, x = mean_biodensity_dm, xmin=minse, xmax=maxse, height = .2))
p1 <- p1 + geom_point(data = gdec, aes(colour = "gray", size =1), show.legend = F ,position = position_nudge(y =0.2)) +
geom_errorbarh(data=gdec, position = position_nudge(y =0.2), aes(y = depth_bin, x = mean_biodensity_dm, xmin=minse, xmax=maxse, height = 0.2, color = "gray"))+
scale_color_manual(values = c("black", "gray"), labels(NULL), guides(fill=FALSE))+ theme_bw()+ ylab("Depth (cm)") +
theme(axis.title.y=element_blank(),
axis.text.y=element_blank(),
axis.ticks.y=element_blank())
p1 <- add_sub(p1, "Dec", x = 0.4, hjust = 0)
p1
adjan <- subset(Jan, Jan$site == 'adenostoma')
gjan <- subset(Jan, Jan$site == 'grass')
p2 <- ggplot(data = adjan, aes(y = depth_bin, x = mean_biodensity_dm)) +
scale_y_continuous(trans = "reverse", breaks = unique(biodensity$depth_bin), labels=c("0-10", "10-20", "20-30", "30-40"))+
scale_x_continuous(position = "top", limits = c(0,.35))+ xlab("")+
geom_point(data = adjan, aes(colour = "black", size =1), show.legend = F ) +
geom_errorbarh(data=adjan, aes(y = depth_bin, x = mean_biodensity_dm, xmin=minse, xmax=maxse, height = .2))
p2 <- p2 + geom_point(data = gjan, aes(colour = "gray", size =1), show.legend = F , position = position_nudge(y =0.2)) +
geom_errorbarh(data=gjan, position = position_nudge(y =0.2), aes(y = depth_bin, x = mean_biodensity_dm, xmin=minse, xmax=maxse, height = 0.2, color = "gray"))+
theme_bw()+
scale_color_manual(values = c("black", "gray"), labels(NULL), guides(fill=FALSE))+ ylab("")+
theme(axis.title.y=element_blank(),
axis.text.y=element_blank(),
axis.ticks.y=element_blank())
p2 <- add_sub(p2, "Jan", x = 0.4, hjust = 0)
p2
adfeb <- subset(Feb, Feb$site == 'adenostoma')
gfeb <- subset(Feb, Feb$site == 'grass')
p3 <- ggplot(data = adfeb, aes(y = depth_bin, x = mean_biodensity_dm))+
scale_y_continuous(trans = "reverse", breaks = unique(biodensity$depth_bin)) +
scale_x_continuous(position = "top", limits = c(0,.35))+ xlab(expression(paste("Root biomass per soil volume (g ", dm^-3, ")"))) +
geom_point(data = adfeb, aes(colour = "black", size =1), show.legend = F ) +
geom_errorbarh(data=adfeb, aes(y = depth_bin, x = mean_biodensity_dm, xmin=minse, xmax=maxse, height = .2))
p3 <- p3 + geom_point(data = gfeb, aes(colour = "gray", size =1), show.legend = F , position = position_nudge(y =0.2)) +
geom_errorbarh(data=gfeb, position = position_nudge(y =0.2), aes(y = depth_bin, x = mean_biodensity_dm, xmin=minse, xmax=maxse, height = 0.2, color = "gray"))+
theme_bw()+ scale_color_manual(values = c("black", "gray"), labels(NULL), guides(fill=FALSE))+ ylab("") +
theme(axis.title.y=element_blank(),
axis.text.y=element_blank(),
axis.ticks.y=element_blank(),
axis.title.x.top = element_text(margin = margin(t = 0, r = 20, b = 0, l = 0)))
p3 <- add_sub(p3, "Feb", x = 0.4, hjust = 0)
p3
admar <- subset(Mar, Mar$site == 'adenostoma')
gmar <- subset(Mar, Mar$site == 'grass')
p4<- ggplot(data = admar, aes(y = depth_bin, x = mean_biodensity_dm)) +
scale_y_continuous(trans = "reverse", breaks = unique(biodensity$depth_bin), labels=c("0-10", "10-20", "20-30", "30-40"))+
scale_x_continuous(position = "top", limits = c(0, .35))+
geom_point(data = admar, aes(colour = "black", size =1), show.legend = F ) +
geom_errorbarh(data=admar, aes(y = depth_bin, x = mean_biodensity_dm, xmin=minse, xmax=maxse, height = .2))
p4 <- p4 + geom_point(data = gmar, aes(colour = "gray", size =1), show.legend = F , position = position_nudge(y =0.2)) +
geom_errorbarh(data=gmar, position = position_nudge(y =0.2), aes(y = depth_bin, x = mean_biodensity_dm, xmin=minse, xmax=maxse, height = 0.2, color = "gray"))+
theme_bw()+ylab("")+ xlab("")+
scale_color_manual(values = c("black", "gray"), labels(NULL), guides(fill=FALSE))+ ylab("") +
theme(axis.title.y=element_blank(),
axis.text.y=element_blank(),
axis.ticks.y=element_blank())
p4 <- add_sub(p4, "Mar", x = 0.4, hjust = 0)
p4
admay <- subset(May, May$site == 'adenostoma')
gmay <- subset(May, May$site == 'grass')
p5<- ggplot(data = admay, aes(y = depth_bin, x = mean_biodensity_dm)) +
scale_y_continuous(trans = "reverse", breaks = unique(biodensity$depth_bin), labels=c("0-10", "10-20", "20-30", "30-40"))+
scale_x_continuous(position = "top", limits = c(0, .35))+
geom_point(data = admay, aes(colour = "black", size =1), show.legend = F ) +
geom_errorbarh(data=admay, aes(y = depth_bin, x = mean_biodensity_dm, xmin=minse, xmax=maxse, height = .2))
p5 <- p5 + geom_point(data = gmay, aes(colour = "gray", size =1), show.legend = F, position = position_nudge(y =0.2)) +
geom_errorbarh(data=gmay, position = position_nudge(y =0.2), aes(y = depth_bin, x = mean_biodensity_dm, xmin=minse, xmax=maxse, height = 0.2, color = "gray"))+
theme_bw()+ylab("")+ scale_color_manual(values = c("black", "gray"), labels(NULL), guides(fill=FALSE))+
xlab("")+
theme(axis.title.y=element_blank(),
axis.text.y=element_blank(),
axis.ticks.y=element_blank())
p5 <- add_sub(p5, "May", x = 0.4, hjust = 0)
grid.arrange(p1, p2, p3, p4, p5, ncol=5)
###############################################################################################
#################now make the same figure by season
library(ggplot2)
library(gridExtra)
library(cowplot)
setwd("D:/R_Workspace/SDEF/SDEF.analysis/data")
load('SDEF_roots_post_aggregation_by_season_v1.rda')
### now by biodensity
biodensity <- SDEF_roots_post_aggregation_by_season_v1
biodensity$mean_biodensity_dm <- biodensity$mean_biodensity*1000
biodensity$sd_biodensity_dm <- biodensity$sd_biodensity*1000
biodensity[is.na(biodensity)] <- 0
biodensity$se_biodensity_dm <- ((biodensity$sd_biodensity_dm)/sqrt(biodensity$n_biodensity))
biodensity$minse <- abs((biodensity$mean_biodensity_dm -biodensity$se_biodensity_dm))
biodensity$maxse <- (biodensity$mean_biodensity_dm +biodensity$se_biodensity_dm)
Espring <- subset(biodensity, biodensity$season_v1 == "Early Spring")
Lspring <- subset(biodensity, biodensity$season_v1 == "Late Spring")
Winter <- subset(biodensity, biodensity$season_v1 == "Winter")
##############
ade <- subset(Espring, Espring$site == 'adenostoma')
ge <- subset(Espring, Espring$site == 'grass')
p1 <- ggplot(data = ade, aes(y = depth_bin, x = mean_biodensity_dm)) +
scale_y_continuous(trans = "reverse", breaks = unique(biodensity$depth_bin), labels=c("0-10", "10-20", "20-30", "30-40")) +
scale_x_continuous(position = "top", limits = c(0, .5)) + xlab(expression(paste("Root biomass (g/", dm^3, ")")))+
geom_point(data = ade, aes(colour = "black", size =1), show.legend = F ) +
geom_errorbarh(data=ade, aes(y = depth_bin, x = mean_biodensity_dm, xmin=minse, xmax=maxse, height = .2))
p1 <- p1 + geom_point(data = ge, aes(colour = "gray", size =1), show.legend = F ,position = position_nudge(y =0.2)) +
geom_errorbarh(data=ge, position = position_nudge(y =0.2), aes(y = depth_bin, x = mean_biodensity_dm, xmin=minse, xmax=maxse, height = 0.2, color = "gray"))+
scale_color_manual(values = c("black", "gray"), labels(NULL), guides(fill=FALSE))+ theme_bw()+ ylab("Depth (cm)") +
theme(axis.title.y=element_blank(),
axis.text.y=element_blank(),
axis.ticks.y=element_blank(),
axis.title.x.top = element_text(margin = margin(t = 0, r = 20, b = 0, l = 0)))
p1 <- add_sub(p1, "Early Spring", x = 0.35, hjust = 0)
p1
adl <- subset(Lspring, Lspring$site == 'adenostoma')
gl <- subset(Lspring, Lspring$site == 'grass')
p2 <- ggplot(data = adl, aes(y = depth_bin, x = mean_biodensity_dm)) +
scale_y_continuous(trans = "reverse", breaks = unique(biodensity$depth_bin), labels=c("0-10", "10-20", "20-30", "30-40"))+
scale_x_continuous(position = "top", limits = c(0,.5))+ xlab("")+
geom_point(data = adl, aes(colour = "black", size =1), show.legend = F ) +
geom_errorbarh(data=adl, aes(y = depth_bin, x = mean_biodensity_dm, xmin=minse, xmax=maxse, height = .2))
p2 <- p2 + geom_point(data = gl, aes(colour = "gray", size =1), show.legend = F , position = position_nudge(y =0.2)) +
geom_errorbarh(data=gl, position = position_nudge(y =0.2), aes(y = depth_bin, x = mean_biodensity_dm, xmin=minse, xmax=maxse, height = 0.2, color = "gray"))+
theme_bw()+
scale_color_manual(values = c("black", "gray"), labels(NULL), guides(fill=FALSE))+ ylab("")+
theme(axis.title.y=element_blank(),
axis.text.y=element_blank(),
axis.ticks.y=element_blank())
p2 <- add_sub(p2, "Late Spring", x = 0.35, hjust = 0)
p2
adw <- subset(Winter, Winter$site == 'adenostoma')
gw <- subset(Winter, Winter$site == 'grass')
p3 <- ggplot(data = adw, aes(y = depth_bin, x = mean_biodensity_dm))+
scale_y_continuous(trans = "reverse", breaks = unique(biodensity$depth_bin)) +
scale_x_continuous(position = "top", limits = c(0,.5))+ xlab("") +
geom_point(data = adw, aes(colour = "black", size =1), show.legend = F ) +
geom_errorbarh(data=adw, aes(y = depth_bin, x = mean_biodensity_dm, xmin=minse, xmax=maxse, height = .2))
p3 <- p3 + geom_point(data = gw, aes(colour = "gray", size =1), show.legend = F , position = position_nudge(y =0.2)) +
geom_errorbarh(data=gw, position = position_nudge(y =0.2), aes(y = depth_bin, x = mean_biodensity_dm, xmin=minse, xmax=maxse, height = 0.2, color = "gray"))+
theme_bw()+ scale_color_manual(values = c("black", "gray"), labels(NULL), guides(fill=FALSE))+ ylab("") +
theme(axis.title.y=element_blank(),
axis.text.y=element_blank(),
axis.ticks.y=element_blank())
p3 <- add_sub(p3, "Winter", x = 0.35, hjust = 0)
p3
grid.arrange( p3, p1, p2, ncol=3)
##################Season V2
library(ggplot2)
library(gridExtra)
library(cowplot)
setwd("D:/R_Workspace/SDEF/SDEF.analysis/data")
load('SDEF_roots_post_aggregation_by_season_v2.rda')
### now by biodensity
biodensity <- SDEF_roots_post_aggregation_by_season_v2
biodensity$mean_biodensity_dm <- biodensity$mean_biodensity*1000
biodensity$sd_biodensity_dm <- biodensity$sd_biodensity*1000
biodensity[is.na(biodensity)] <- 0
biodensity$se_biodensity_dm <- ((biodensity$sd_biodensity_dm)/sqrt(biodensity$n_biodensity))
biodensity$minse <- abs((biodensity$mean_biodensity_dm -biodensity$se_biodensity_dm))
biodensity$maxse <- (biodensity$mean_biodensity_dm +biodensity$se_biodensity_dm)
Espring <- subset(biodensity, biodensity$season_v2 == "Early Spring")
Mar <- subset(biodensity, biodensity$season_v2 == "Mar")
May <- subset(biodensity, biodensity$season_v2 == "May")
Winter <- subset(biodensity, biodensity$season_v2 == "Winter")
##############
ade <- subset(Espring, Espring$site == 'adenostoma')
ge <- subset(Espring, Espring$site == 'grass')
p1 <- ggplot(data = ade, aes(y = depth_bin, x = mean_biodensity_dm)) +
scale_y_continuous(trans = "reverse", breaks = unique(biodensity$depth_bin), labels=c("0-10", "10-20", "20-30", "30-40")) +
scale_x_continuous(position = "top", limits = c(0, .4)) + xlab("")+
geom_point(data = ade, aes(colour = "black", size =1), show.legend = F ) +
geom_errorbarh(data=ade, aes(y = depth_bin, x = mean_biodensity_dm, xmin=minse, xmax=maxse, height = .2))
p1 <- p1 + geom_point(data = ge, aes(colour = "gray", size =1), show.legend = F ,position = position_nudge(y =0.2)) +
geom_errorbarh(data=ge, position = position_nudge(y =0.2), aes(y = depth_bin, x = mean_biodensity_dm, xmin=minse, xmax=maxse, height = 0.2, color = "gray"))+
scale_color_manual(values = c("black", "gray"), labels(NULL), guides(fill=FALSE))+ theme_bw()+ ylab("Depth (cm)") +
theme(axis.title.y=element_blank(),
axis.text.y=element_blank(),
axis.ticks.y=element_blank())
p1 <- add_sub(p1, "Early Spring", x = 0.2, hjust = 0)
p1
admar <- subset(Mar, Mar$site == 'adenostoma')
gmar <- subset(Mar, Mar$site == 'grass')
p2 <- ggplot(data = admar, aes(y = depth_bin, x = mean_biodensity_dm)) +
scale_y_continuous(trans = "reverse", breaks = unique(biodensity$depth_bin), labels=c("0-10", "10-20", "20-30", "30-40"))+
scale_x_continuous(position = "top", limits = c(0,.4))+ xlab("")+
geom_point(data = admar, aes(colour = "black", size =1), show.legend = F ) +
geom_errorbarh(data=admar, aes(y = depth_bin, x = mean_biodensity_dm, xmin=minse, xmax=maxse, height = .2))
p2 <- p2 + geom_point(data = gmar, aes(colour = "gray", size =1), show.legend = F , position = position_nudge(y =0.2)) +
geom_errorbarh(data=gmar, position = position_nudge(y =0.2), aes(y = depth_bin, x = mean_biodensity_dm, xmin=minse, xmax=maxse, height = 0.2, color = "gray"))+
theme_bw()+
scale_color_manual(values = c("black", "gray"), labels(NULL), guides(fill=FALSE))+ ylab("")+
theme(axis.title.y=element_blank(),
axis.text.y=element_blank(),
axis.ticks.y=element_blank())
p2 <- add_sub(p2, "March", x = 0.35, hjust = 0)
p2
adw <- subset(Winter, Winter$site == 'adenostoma')
gw <- subset(Winter, Winter$site == 'grass')
p3 <- ggplot(data = adw, aes(y = depth_bin, x = mean_biodensity_dm))+
scale_y_continuous(trans = "reverse", breaks = unique(biodensity$depth_bin)) +
scale_x_continuous(position = "top", limits = c(0,.4))+ xlab("") +
geom_point(data = adw, aes(colour = "black", size =1), show.legend = F ) +
geom_errorbarh(data=adw, aes(y = depth_bin, x = mean_biodensity_dm, xmin=minse, xmax=maxse, height = .2))
p3 <- p3 + geom_point(data = gw, aes(colour = "gray", size =1), show.legend = F , position = position_nudge(y =0.2)) +
geom_errorbarh(data=gw, position = position_nudge(y =0.2), aes(y = depth_bin, x = mean_biodensity_dm, xmin=minse, xmax=maxse, height = 0.2, color = "gray"))+
theme_bw()+ scale_color_manual(values = c("black", "gray"), labels(NULL), guides(fill=FALSE))+ ylab("") +
theme(axis.title.y=element_blank(),
axis.text.y=element_blank(),
axis.ticks.y=element_blank())
p3 <- add_sub(p3, "Winter", x = 0.35, hjust = 0)
p3
admay <- subset(May, May$site == 'adenostoma')
gmay <- subset(May, May$site == 'grass')
p4 <- ggplot(data = admay, aes(y = depth_bin, x = mean_biodensity_dm)) +
scale_y_continuous(trans = "reverse", breaks = unique(biodensity$depth_bin), labels=c("0-10", "10-20", "20-30", "30-40"))+
scale_x_continuous(position = "top", limits = c(0,.4))+ xlab("")+
geom_point(data = admay, aes(colour = "black", size =1), show.legend = F ) +
geom_errorbarh(data=admay, aes(y = depth_bin, x = mean_biodensity_dm, xmin=minse, xmax=maxse, height = .2))
p4 <- p4 + geom_point(data = gmay, aes(colour = "gray", size =1), show.legend = F , position = position_nudge(y =0.2)) +
geom_errorbarh(data=gmay, position = position_nudge(y =0.2), aes(y = depth_bin, x = mean_biodensity_dm, xmin=minse, xmax=maxse, height = 0.2, color = "gray"))+
theme_bw()+
scale_color_manual(values = c("black", "gray"), labels(NULL), guides(fill=FALSE))+ ylab("")+
theme(axis.title.y=element_blank(),
axis.text.y=element_blank(),
axis.ticks.y=element_blank())
p4 <- add_sub(p4, "May", x = 0.35, hjust = 0)
p4
grid.arrange( p3, p1, p2, p4, ncol=4)
##################Season V3
library(ggplot2)
library(gridExtra)
library(cowplot)
setwd("D:/R_Workspace/SDEF/SDEF.analysis/data")
load('SDEF_roots_post_aggregation_by_season_v3.rda')
### now by biodensity
biodensity <- SDEF_roots_post_aggregation_by_season_v3
biodensity$mean_biodensity_dm <- biodensity$mean_biodensity*1000
biodensity$sd_biodensity_dm <- biodensity$sd_biodensity*1000
biodensity[is.na(biodensity)] <- 0
biodensity$se_biodensity_dm <- ((biodensity$sd_biodensity_dm)/sqrt(biodensity$n_biodensity))
biodensity$minse <- abs((biodensity$mean_biodensity_dm -biodensity$se_biodensity_dm))
biodensity$maxse <- (biodensity$mean_biodensity_dm +biodensity$se_biodensity_dm)
Espring <- subset(biodensity, biodensity$season_v3 == "Early Spring")
May <- subset(biodensity, biodensity$season_v3 == "May")
Winter <- subset(biodensity, biodensity$season_v3 == "Winter")
##############
ade <- subset(Espring, Espring$site == 'adenostoma')
ge <- subset(Espring, Espring$site == 'grass')
p1 <- ggplot(data = ade, aes(y = depth_bin, x = mean_biodensity_dm)) +
scale_y_continuous(trans = "reverse", breaks = unique(biodensity$depth_bin), labels=c("0-10", "10-20", "20-30", "30-40")) +
scale_x_continuous(position = "top", limits = c(0, .4)) + xlab("")+
geom_point(data = ade, aes(colour = "black", size =1), show.legend = F ) +
geom_errorbarh(data=ade, aes(y = depth_bin, x = mean_biodensity_dm, xmin=minse, xmax=maxse, height = .2))
p1 <- p1 + geom_point(data = ge, aes(colour = "gray", size =1), show.legend = F ,position = position_nudge(y =0.2)) +
geom_errorbarh(data=ge, position = position_nudge(y =0.2), aes(y = depth_bin, x = mean_biodensity_dm, xmin=minse, xmax=maxse, height = 0.2, color = "gray"))+
scale_color_manual(values = c("black", "gray"), labels(NULL), guides(fill=FALSE))+ theme_bw()+ ylab("Depth (cm)") +
theme(axis.title.y=element_blank(),
axis.text.y=element_blank(),
axis.ticks.y=element_blank())
p1 <- add_sub(p1, "Early Spring", x = 0.2, hjust = 0)
p1
adw <- subset(Winter, Winter$site == 'adenostoma')
gw <- subset(Winter, Winter$site == 'grass')
p3 <- ggplot(data = adw, aes(y = depth_bin, x = mean_biodensity_dm))+
scale_y_continuous(trans = "reverse", breaks = unique(biodensity$depth_bin)) +
scale_x_continuous(position = "top", limits = c(0,.4))+ xlab("") +
geom_point(data = adw, aes(colour = "black", size =1), show.legend = F ) +
geom_errorbarh(data=adw, aes(y = depth_bin, x = mean_biodensity_dm, xmin=minse, xmax=maxse, height = .2))
p3 <- p3 + geom_point(data = gw, aes(colour = "gray", size =1), show.legend = F , position = position_nudge(y =0.2)) +
geom_errorbarh(data=gw, position = position_nudge(y =0.2), aes(y = depth_bin, x = mean_biodensity_dm, xmin=minse, xmax=maxse, height = 0.2, color = "gray"))+
theme_bw()+ scale_color_manual(values = c("black", "gray"), labels(NULL), guides(fill=FALSE))+ ylab("") +
theme(axis.title.y=element_blank(),
axis.text.y=element_blank(),
axis.ticks.y=element_blank())
p3 <- add_sub(p3, "Winter", x = 0.35, hjust = 0)
p3
admay <- subset(May, May$site == 'adenostoma')
gmay <- subset(May, May$site == 'grass')
p4 <- ggplot(data = admay, aes(y = depth_bin, x = mean_biodensity_dm)) +
scale_y_continuous(trans = "reverse", breaks = unique(biodensity$depth_bin), labels=c("0-10", "10-20", "20-30", "30-40"))+
scale_x_continuous(position = "top", limits = c(0,.4))+ xlab("")+
geom_point(data = admay, aes(colour = "black", size =1), show.legend = F ) +
geom_errorbarh(data=admay, aes(y = depth_bin, x = mean_biodensity_dm, xmin=minse, xmax=maxse, height = .2))
p4 <- p4 + geom_point(data = gmay, aes(colour = "gray", size =1), show.legend = F , position = position_nudge(y =0.2)) +
geom_errorbarh(data=gmay, position = position_nudge(y =0.2), aes(y = depth_bin, x = mean_biodensity_dm, xmin=minse, xmax=maxse, height = 0.2, color = "gray"))+
theme_bw()+
scale_color_manual(values = c("black", "gray"), labels(NULL), guides(fill=FALSE))+ ylab("")+
theme(axis.title.y=element_blank(),
axis.text.y=element_blank(),
axis.ticks.y=element_blank())
p4 <- add_sub(p4, "May", x = 0.35, hjust = 0)
p4
grid.arrange( p3, p1, p4, ncol=3)
bmcnellis/SDEF.analysis documentation built on June 4, 2019, 10 a.m.
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### Visualize root data : Figure 4
library(ggplot2)
library(gridExtra)
library(cowplot)
setwd("D:/R_Workspace/SDEF/SDEF.analysis/data")
load('SDEF_roots_post_aggregation_by_month.rda')
### Root length figures
biodensity <- SDEF_roots_post_aggregation_by_month
biodensity[is.na(biodensity)] <- 0
biodensity$se_length <- ((biodensity$sd_length)/sqrt(biodensity$n_length))
biodensity$minse <- abs((biodensity$mean_length -biodensity$se_length))
biodensity$maxse <- (biodensity$mean_length +biodensity$se_length)
#subset by month for graphing
Dec <- subset(biodensity, biodensity$month == "Dec")
Jan <- subset(biodensity, biodensity$month == "Jan")
Feb <- subset(biodensity, biodensity$month == "Feb")
Mar <- subset(biodensity, biodensity$month == "Mar")
May <- subset(biodensity, biodensity$month == "May")
##############
addec <- subset(Dec, Dec$site == 'adenostoma')
gdec <- subset(Dec, Dec$site == 'grass')
p1 <- ggplot(data = addec, aes(y = depth_bin, x = mean_length)) +
scale_y_continuous(trans = "reverse", breaks = unique(biodensity$depth_bin), labels=c("0-10", "10-20", "20-30", "30-40")) +
scale_x_continuous(position = "top", limits = c(0, 9)) + xlab("")+
geom_point(data = addec, aes(colour = "black", size =1), show.legend = F ) +
geom_errorbarh(data=addec, aes(y = depth_bin, x = mean_length, xmin=minse, xmax=maxse, height = .2))
p1 <- p1 + geom_point(data = gdec, aes(colour = "gray", size =1), show.legend = F ,position = position_nudge(y =0.2)) +
geom_errorbarh(data=gdec, position = position_nudge(y =0.2), aes(y = depth_bin, x = mean_length, xmin=minse, xmax=maxse, height = 0.2, color = "gray"))+
scale_color_manual(values = c("black", "gray"), labels(NULL), guides(fill=FALSE))+ theme_bw()+ ylab("Depth (cm)") +
theme(axis.title.y=element_blank(),
axis.text.y=element_blank(),
axis.ticks.y=element_blank())
p1 <- add_sub(p1, "Dec", x = 4.5, hjust = 0)
p1
adjan <- subset(Jan, Jan$site == 'adenostoma')
gjan <- subset(Jan, Jan$site == 'grass')
p2 <- ggplot(data = adjan, aes(y = depth_bin, x = mean_length)) +
scale_y_continuous(trans = "reverse", breaks = unique(biodensity$depth_bin), labels=c("0-10", "10-20", "20-30", "30-40"))+
scale_x_continuous(position = "top", limits = c(0,9))+ xlab("")+
geom_point(data = adjan, aes(colour = "black", size =1), show.legend = F ) +
geom_errorbarh(data=adjan, aes(y = depth_bin, x = mean_length, xmin=minse, xmax=maxse, height = .2))
p2 <- p2 + geom_point(data = gjan, aes(colour = "gray", size =1), show.legend = F , position = position_nudge(y =0.2)) +
geom_errorbarh(data=gjan, position = position_nudge(y =0.2), aes(y = depth_bin, x = mean_length, xmin=minse, xmax=maxse, height = 0.2, color = "gray"))+
theme_bw()+
scale_color_manual(values = c("black", "gray"), labels(NULL), guides(fill=FALSE))+ ylab("")+
theme(axis.title.y=element_blank(),
axis.text.y=element_blank(),
axis.ticks.y=element_blank())
p2 <- add_sub(p2, "Jan", x = 4.5, hjust = 0)
p2
adfeb <- subset(Feb, Feb$site == 'adenostoma')
gfeb <- subset(Feb, Feb$site == 'grass')
p3 <- ggplot(data = adfeb, aes(y = depth_bin, x = mean_length))+
scale_y_continuous(trans = "reverse", breaks = unique(biodensity$depth_bin)) +
scale_x_continuous(position = "top", limits = c(0,9))+ xlab(expression(paste("Mean root length (mm)"))) +
geom_point(data = adfeb, aes(colour = "black", size =1), show.legend = F ) +
geom_errorbarh(data=adfeb, aes(y = depth_bin, x = mean_length, xmin=minse, xmax=maxse, height = .2))
p3 <- p3 + geom_point(data = gfeb, aes(colour = "gray", size =1), show.legend = F , position = position_nudge(y =0.2)) +
geom_errorbarh(data=gfeb, position = position_nudge(y =0.2), aes(y = depth_bin, x = mean_length, xmin=minse, xmax=maxse, height = 0.2, color = "gray"))+
theme_bw()+ scale_color_manual(values = c("black", "gray"), labels(NULL), guides(fill=FALSE))+ ylab("") +
theme(axis.title.y=element_blank(),
axis.text.y=element_blank(),
axis.ticks.y=element_blank(),
axis.title.x.top = element_text(margin = margin(t = 0, r = 20, b = 0, l = 0)))
p3 <- add_sub(p3, "Feb", x = 4.5, hjust = 0)
p3
admar <- subset(Mar, Mar$site == 'adenostoma')
gmar <- subset(Mar, Mar$site == 'grass')
p4<- ggplot(data = admar, aes(y = depth_bin, x = mean_length)) +
scale_y_continuous(trans = "reverse", breaks = unique(biodensity$depth_bin), labels=c("0-10", "10-20", "20-30", "30-40"))+
scale_x_continuous(position = "top", limits = c(0, 9))+
geom_point(data = admar, aes(colour = "black", size =1), show.legend = F ) +
geom_errorbarh(data=admar, aes(y = depth_bin, x = mean_length, xmin=minse, xmax=maxse, height = .2))
p4 <- p4 + geom_point(data = gmar, aes(colour = "gray", size =1), show.legend = F , position = position_nudge(y =0.2)) +
geom_errorbarh(data=gmar, position = position_nudge(y =0.2), aes(y = depth_bin, x = mean_length, xmin=minse, xmax=maxse, height = 0.2, color = "gray"))+
theme_bw()+ylab("")+ xlab("")+
scale_color_manual(values = c("black", "gray"), labels(NULL), guides(fill=FALSE))+ ylab("") +
theme(axis.title.y=element_blank(),
axis.text.y=element_blank(),
axis.ticks.y=element_blank())
p4 <- add_sub(p4, "Mar", x = 4.5, hjust = 0)
p4
admay <- subset(May, May$site == 'adenostoma')
gmay <- subset(May, May$site == 'grass')
p5<- ggplot(data = admay, aes(y = depth_bin, x = mean_length)) +
scale_y_continuous(trans = "reverse", breaks = unique(biodensity$depth_bin), labels=c("0-10", "10-20", "20-30", "30-40"))+
scale_x_continuous(position = "top", limits = c(0, 9))+
geom_point(data = admay, aes(colour = "black", size =1), show.legend = F ) +
geom_errorbarh(data=admay, aes(y = depth_bin, x = mean_length, xmin=minse, xmax=maxse, height = .2))
p5 <- p5 + geom_point(data = gmay, aes(colour = "gray", size =1), show.legend = F, position = position_nudge(y =0.2)) +
geom_errorbarh(data=gmay, position = position_nudge(y =0.2), aes(y = depth_bin, x = mean_length, xmin=minse, xmax=maxse, height = 0.2, color = "gray"))+
theme_bw()+ylab("")+ scale_color_manual(values = c("black", "gray"), labels(NULL), guides(fill=FALSE))+
xlab("")+
theme(axis.title.y=element_blank(),
axis.text.y=element_blank(),
axis.ticks.y=element_blank())
p5 <- add_sub(p5, "May", x = 4.5, hjust = 0)
grid.arrange(p1, p2, p3, p4, p5, ncol=5)
######## Root biomass figures
biodensity$mean_biodensity_dm <- biodensity$mean_biodensity*1000
biodensity$sd_biodensity_dm <- biodensity$sd_biodensity*1000
biodensity[is.na(biodensity)] <- 0
biodensity$se_biodensity_dm <- ((biodensity$sd_biodensity_dm)/sqrt(biodensity$n_biodensity))
biodensity$minse <- abs((biodensity$mean_biodensity_dm -biodensity$se_biodensity_dm))
biodensity$maxse <- (biodensity$mean_biodensity_dm +biodensity$se_biodensity_dm)
Dec <- subset(biodensity, biodensity$month == "Dec")
Jan <- subset(biodensity, biodensity$month == "Jan")
Feb <- subset(biodensity, biodensity$month == "Feb")
Mar <- subset(biodensity, biodensity$month == "Mar")
May <- subset(biodensity, biodensity$month == "May")
##############
addec <- subset(Dec, Dec$site == 'adenostoma')
gdec <- subset(Dec, Dec$site == 'grass')
p1 <- ggplot(data = addec, aes(y = depth_bin, x = mean_biodensity_dm)) +
scale_y_continuous(trans = "reverse", breaks = unique(biodensity$depth_bin), labels=c("0-10", "10-20", "20-30", "30-40")) +
scale_x_continuous(position = "top", limits = c(0, .35)) + xlab("")+
geom_point(data = addec, aes(colour = "black", size =1), show.legend = F ) +
geom_errorbarh(data=addec, aes(y = depth_bin, x = mean_biodensity_dm, xmin=minse, xmax=maxse, height = .2))
p1 <- p1 + geom_point(data = gdec, aes(colour = "gray", size =1), show.legend = F ,position = position_nudge(y =0.2)) +
geom_errorbarh(data=gdec, position = position_nudge(y =0.2), aes(y = depth_bin, x = mean_biodensity_dm, xmin=minse, xmax=maxse, height = 0.2, color = "gray"))+
scale_color_manual(values = c("black", "gray"), labels(NULL), guides(fill=FALSE))+ theme_bw()+ ylab("Depth (cm)") +
theme(axis.title.y=element_blank(),
axis.text.y=element_blank(),
axis.ticks.y=element_blank())
p1 <- add_sub(p1, "Dec", x = 0.4, hjust = 0)
p1
adjan <- subset(Jan, Jan$site == 'adenostoma')
gjan <- subset(Jan, Jan$site == 'grass')
p2 <- ggplot(data = adjan, aes(y = depth_bin, x = mean_biodensity_dm)) +
scale_y_continuous(trans = "reverse", breaks = unique(biodensity$depth_bin), labels=c("0-10", "10-20", "20-30", "30-40"))+
scale_x_continuous(position = "top", limits = c(0,.35))+ xlab("")+
geom_point(data = adjan, aes(colour = "black", size =1), show.legend = F ) +
geom_errorbarh(data=adjan, aes(y = depth_bin, x = mean_biodensity_dm, xmin=minse, xmax=maxse, height = .2))
p2 <- p2 + geom_point(data = gjan, aes(colour = "gray", size =1), show.legend = F , position = position_nudge(y =0.2)) +
geom_errorbarh(data=gjan, position = position_nudge(y =0.2), aes(y = depth_bin, x = mean_biodensity_dm, xmin=minse, xmax=maxse, height = 0.2, color = "gray"))+
theme_bw()+
scale_color_manual(values = c("black", "gray"), labels(NULL), guides(fill=FALSE))+ ylab("")+
theme(axis.title.y=element_blank(),
axis.text.y=element_blank(),
axis.ticks.y=element_blank())
p2 <- add_sub(p2, "Jan", x = 0.4, hjust = 0)
p2
adfeb <- subset(Feb, Feb$site == 'adenostoma')
gfeb <- subset(Feb, Feb$site == 'grass')
p3 <- ggplot(data = adfeb, aes(y = depth_bin, x = mean_biodensity_dm))+
scale_y_continuous(trans = "reverse", breaks = unique(biodensity$depth_bin)) +
scale_x_continuous(position = "top", limits = c(0,.35))+ xlab(expression(paste("Root biomass per soil volume (g ", dm^-3, ")"))) +
geom_point(data = adfeb, aes(colour = "black", size =1), show.legend = F ) +
geom_errorbarh(data=adfeb, aes(y = depth_bin, x = mean_biodensity_dm, xmin=minse, xmax=maxse, height = .2))
p3 <- p3 + geom_point(data = gfeb, aes(colour = "gray", size =1), show.legend = F , position = position_nudge(y =0.2)) +
geom_errorbarh(data=gfeb, position = position_nudge(y =0.2), aes(y = depth_bin, x = mean_biodensity_dm, xmin=minse, xmax=maxse, height = 0.2, color = "gray"))+
theme_bw()+ scale_color_manual(values = c("black", "gray"), labels(NULL), guides(fill=FALSE))+ ylab("") +
theme(axis.title.y=element_blank(),
axis.text.y=element_blank(),
axis.ticks.y=element_blank(),
axis.title.x.top = element_text(margin = margin(t = 0, r = 20, b = 0, l = 0)))
p3 <- add_sub(p3, "Feb", x = 0.4, hjust = 0)
p3
admar <- subset(Mar, Mar$site == 'adenostoma')
gmar <- subset(Mar, Mar$site == 'grass')
p4<- ggplot(data = admar, aes(y = depth_bin, x = mean_biodensity_dm)) +
scale_y_continuous(trans = "reverse", breaks = unique(biodensity$depth_bin), labels=c("0-10", "10-20", "20-30", "30-40"))+
scale_x_continuous(position = "top", limits = c(0, .35))+
geom_point(data = admar, aes(colour = "black", size =1), show.legend = F ) +
geom_errorbarh(data=admar, aes(y = depth_bin, x = mean_biodensity_dm, xmin=minse, xmax=maxse, height = .2))
p4 <- p4 + geom_point(data = gmar, aes(colour = "gray", size =1), show.legend = F , position = position_nudge(y =0.2)) +
geom_errorbarh(data=gmar, position = position_nudge(y =0.2), aes(y = depth_bin, x = mean_biodensity_dm, xmin=minse, xmax=maxse, height = 0.2, color = "gray"))+
theme_bw()+ylab("")+ xlab("")+
scale_color_manual(values = c("black", "gray"), labels(NULL), guides(fill=FALSE))+ ylab("") +
theme(axis.title.y=element_blank(),
axis.text.y=element_blank(),
axis.ticks.y=element_blank())
p4 <- add_sub(p4, "Mar", x = 0.4, hjust = 0)
p4
admay <- subset(May, May$site == 'adenostoma')
gmay <- subset(May, May$site == 'grass')
p5<- ggplot(data = admay, aes(y = depth_bin, x = mean_biodensity_dm)) +
scale_y_continuous(trans = "reverse", breaks = unique(biodensity$depth_bin), labels=c("0-10", "10-20", "20-30", "30-40"))+
scale_x_continuous(position = "top", limits = c(0, .35))+
geom_point(data = admay, aes(colour = "black", size =1), show.legend = F ) +
geom_errorbarh(data=admay, aes(y = depth_bin, x = mean_biodensity_dm, xmin=minse, xmax=maxse, height = .2))
p5 <- p5 + geom_point(data = gmay, aes(colour = "gray", size =1), show.legend = F, position = position_nudge(y =0.2)) +
geom_errorbarh(data=gmay, position = position_nudge(y =0.2), aes(y = depth_bin, x = mean_biodensity_dm, xmin=minse, xmax=maxse, height = 0.2, color = "gray"))+
theme_bw()+ylab("")+ scale_color_manual(values = c("black", "gray"), labels(NULL), guides(fill=FALSE))+
xlab("")+
theme(axis.title.y=element_blank(),
axis.text.y=element_blank(),
axis.ticks.y=element_blank())
p5 <- add_sub(p5, "May", x = 0.4, hjust = 0)
grid.arrange(p1, p2, p3, p4, p5, ncol=5)
###############################################################################################
#################now make the same figure by season
library(ggplot2)
library(gridExtra)
library(cowplot)
setwd("D:/R_Workspace/SDEF/SDEF.analysis/data")
load('SDEF_roots_post_aggregation_by_season_v1.rda')
### now by biodensity
biodensity <- SDEF_roots_post_aggregation_by_season_v1
biodensity$mean_biodensity_dm <- biodensity$mean_biodensity*1000
biodensity$sd_biodensity_dm <- biodensity$sd_biodensity*1000
biodensity[is.na(biodensity)] <- 0
biodensity$se_biodensity_dm <- ((biodensity$sd_biodensity_dm)/sqrt(biodensity$n_biodensity))
biodensity$minse <- abs((biodensity$mean_biodensity_dm -biodensity$se_biodensity_dm))
biodensity$maxse <- (biodensity$mean_biodensity_dm +biodensity$se_biodensity_dm)
Espring <- subset(biodensity, biodensity$season_v1 == "Early Spring")
Lspring <- subset(biodensity, biodensity$season_v1 == "Late Spring")
Winter <- subset(biodensity, biodensity$season_v1 == "Winter")
##############
ade <- subset(Espring, Espring$site == 'adenostoma')
ge <- subset(Espring, Espring$site == 'grass')
p1 <- ggplot(data = ade, aes(y = depth_bin, x = mean_biodensity_dm)) +
scale_y_continuous(trans = "reverse", breaks = unique(biodensity$depth_bin), labels=c("0-10", "10-20", "20-30", "30-40")) +
scale_x_continuous(position = "top", limits = c(0, .5)) + xlab(expression(paste("Root biomass (g/", dm^3, ")")))+
geom_point(data = ade, aes(colour = "black", size =1), show.legend = F ) +
geom_errorbarh(data=ade, aes(y = depth_bin, x = mean_biodensity_dm, xmin=minse, xmax=maxse, height = .2))
p1 <- p1 + geom_point(data = ge, aes(colour = "gray", size =1), show.legend = F ,position = position_nudge(y =0.2)) +
geom_errorbarh(data=ge, position = position_nudge(y =0.2), aes(y = depth_bin, x = mean_biodensity_dm, xmin=minse, xmax=maxse, height = 0.2, color = "gray"))+
scale_color_manual(values = c("black", "gray"), labels(NULL), guides(fill=FALSE))+ theme_bw()+ ylab("Depth (cm)") +
theme(axis.title.y=element_blank(),
axis.text.y=element_blank(),
axis.ticks.y=element_blank(),
axis.title.x.top = element_text(margin = margin(t = 0, r = 20, b = 0, l = 0)))
p1 <- add_sub(p1, "Early Spring", x = 0.35, hjust = 0)
p1
adl <- subset(Lspring, Lspring$site == 'adenostoma')
gl <- subset(Lspring, Lspring$site == 'grass')
p2 <- ggplot(data = adl, aes(y = depth_bin, x = mean_biodensity_dm)) +
scale_y_continuous(trans = "reverse", breaks = unique(biodensity$depth_bin), labels=c("0-10", "10-20", "20-30", "30-40"))+
scale_x_continuous(position = "top", limits = c(0,.5))+ xlab("")+
geom_point(data = adl, aes(colour = "black", size =1), show.legend = F ) +
geom_errorbarh(data=adl, aes(y = depth_bin, x = mean_biodensity_dm, xmin=minse, xmax=maxse, height = .2))
p2 <- p2 + geom_point(data = gl, aes(colour = "gray", size =1), show.legend = F , position = position_nudge(y =0.2)) +
geom_errorbarh(data=gl, position = position_nudge(y =0.2), aes(y = depth_bin, x = mean_biodensity_dm, xmin=minse, xmax=maxse, height = 0.2, color = "gray"))+
theme_bw()+
scale_color_manual(values = c("black", "gray"), labels(NULL), guides(fill=FALSE))+ ylab("")+
theme(axis.title.y=element_blank(),
axis.text.y=element_blank(),
axis.ticks.y=element_blank())
p2 <- add_sub(p2, "Late Spring", x = 0.35, hjust = 0)
p2
adw <- subset(Winter, Winter$site == 'adenostoma')
gw <- subset(Winter, Winter$site == 'grass')
p3 <- ggplot(data = adw, aes(y = depth_bin, x = mean_biodensity_dm))+
scale_y_continuous(trans = "reverse", breaks = unique(biodensity$depth_bin)) +
scale_x_continuous(position = "top", limits = c(0,.5))+ xlab("") +
geom_point(data = adw, aes(colour = "black", size =1), show.legend = F ) +
geom_errorbarh(data=adw, aes(y = depth_bin, x = mean_biodensity_dm, xmin=minse, xmax=maxse, height = .2))
p3 <- p3 + geom_point(data = gw, aes(colour = "gray", size =1), show.legend = F , position = position_nudge(y =0.2)) +
geom_errorbarh(data=gw, position = position_nudge(y =0.2), aes(y = depth_bin, x = mean_biodensity_dm, xmin=minse, xmax=maxse, height = 0.2, color = "gray"))+
theme_bw()+ scale_color_manual(values = c("black", "gray"), labels(NULL), guides(fill=FALSE))+ ylab("") +
theme(axis.title.y=element_blank(),
axis.text.y=element_blank(),
axis.ticks.y=element_blank())
p3 <- add_sub(p3, "Winter", x = 0.35, hjust = 0)
p3
grid.arrange( p3, p1, p2, ncol=3)
##################Season V2
library(ggplot2)
library(gridExtra)
library(cowplot)
setwd("D:/R_Workspace/SDEF/SDEF.analysis/data")
load('SDEF_roots_post_aggregation_by_season_v2.rda')
### now by biodensity
biodensity <- SDEF_roots_post_aggregation_by_season_v2
biodensity$mean_biodensity_dm <- biodensity$mean_biodensity*1000
biodensity$sd_biodensity_dm <- biodensity$sd_biodensity*1000
biodensity[is.na(biodensity)] <- 0
biodensity$se_biodensity_dm <- ((biodensity$sd_biodensity_dm)/sqrt(biodensity$n_biodensity))
biodensity$minse <- abs((biodensity$mean_biodensity_dm -biodensity$se_biodensity_dm))
biodensity$maxse <- (biodensity$mean_biodensity_dm +biodensity$se_biodensity_dm)
Espring <- subset(biodensity, biodensity$season_v2 == "Early Spring")
Mar <- subset(biodensity, biodensity$season_v2 == "Mar")
May <- subset(biodensity, biodensity$season_v2 == "May")
Winter <- subset(biodensity, biodensity$season_v2 == "Winter")
##############
ade <- subset(Espring, Espring$site == 'adenostoma')
ge <- subset(Espring, Espring$site == 'grass')
p1 <- ggplot(data = ade, aes(y = depth_bin, x = mean_biodensity_dm)) +
scale_y_continuous(trans = "reverse", breaks = unique(biodensity$depth_bin), labels=c("0-10", "10-20", "20-30", "30-40")) +
scale_x_continuous(position = "top", limits = c(0, .4)) + xlab("")+
geom_point(data = ade, aes(colour = "black", size =1), show.legend = F ) +
geom_errorbarh(data=ade, aes(y = depth_bin, x = mean_biodensity_dm, xmin=minse, xmax=maxse, height = .2))
p1 <- p1 + geom_point(data = ge, aes(colour = "gray", size =1), show.legend = F ,position = position_nudge(y =0.2)) +
geom_errorbarh(data=ge, position = position_nudge(y =0.2), aes(y = depth_bin, x = mean_biodensity_dm, xmin=minse, xmax=maxse, height = 0.2, color = "gray"))+
scale_color_manual(values = c("black", "gray"), labels(NULL), guides(fill=FALSE))+ theme_bw()+ ylab("Depth (cm)") +
theme(axis.title.y=element_blank(),
axis.text.y=element_blank(),
axis.ticks.y=element_blank())
p1 <- add_sub(p1, "Early Spring", x = 0.2, hjust = 0)
p1
admar <- subset(Mar, Mar$site == 'adenostoma')
gmar <- subset(Mar, Mar$site == 'grass')
p2 <- ggplot(data = admar, aes(y = depth_bin, x = mean_biodensity_dm)) +
scale_y_continuous(trans = "reverse", breaks = unique(biodensity$depth_bin), labels=c("0-10", "10-20", "20-30", "30-40"))+
scale_x_continuous(position = "top", limits = c(0,.4))+ xlab("")+
geom_point(data = admar, aes(colour = "black", size =1), show.legend = F ) +
geom_errorbarh(data=admar, aes(y = depth_bin, x = mean_biodensity_dm, xmin=minse, xmax=maxse, height = .2))
p2 <- p2 + geom_point(data = gmar, aes(colour = "gray", size =1), show.legend = F , position = position_nudge(y =0.2)) +
geom_errorbarh(data=gmar, position = position_nudge(y =0.2), aes(y = depth_bin, x = mean_biodensity_dm, xmin=minse, xmax=maxse, height = 0.2, color = "gray"))+
theme_bw()+
scale_color_manual(values = c("black", "gray"), labels(NULL), guides(fill=FALSE))+ ylab("")+
theme(axis.title.y=element_blank(),
axis.text.y=element_blank(),
axis.ticks.y=element_blank())
p2 <- add_sub(p2, "March", x = 0.35, hjust = 0)
p2
adw <- subset(Winter, Winter$site == 'adenostoma')
gw <- subset(Winter, Winter$site == 'grass')
p3 <- ggplot(data = adw, aes(y = depth_bin, x = mean_biodensity_dm))+
scale_y_continuous(trans = "reverse", breaks = unique(biodensity$depth_bin)) +
scale_x_continuous(position = "top", limits = c(0,.4))+ xlab("") +
geom_point(data = adw, aes(colour = "black", size =1), show.legend = F ) +
geom_errorbarh(data=adw, aes(y = depth_bin, x = mean_biodensity_dm, xmin=minse, xmax=maxse, height = .2))
p3 <- p3 + geom_point(data = gw, aes(colour = "gray", size =1), show.legend = F , position = position_nudge(y =0.2)) +
geom_errorbarh(data=gw, position = position_nudge(y =0.2), aes(y = depth_bin, x = mean_biodensity_dm, xmin=minse, xmax=maxse, height = 0.2, color = "gray"))+
theme_bw()+ scale_color_manual(values = c("black", "gray"), labels(NULL), guides(fill=FALSE))+ ylab("") +
theme(axis.title.y=element_blank(),
axis.text.y=element_blank(),
axis.ticks.y=element_blank())
p3 <- add_sub(p3, "Winter", x = 0.35, hjust = 0)
p3
admay <- subset(May, May$site == 'adenostoma')
gmay <- subset(May, May$site == 'grass')
p4 <- ggplot(data = admay, aes(y = depth_bin, x = mean_biodensity_dm)) +
scale_y_continuous(trans = "reverse", breaks = unique(biodensity$depth_bin), labels=c("0-10", "10-20", "20-30", "30-40"))+
scale_x_continuous(position = "top", limits = c(0,.4))+ xlab("")+
geom_point(data = admay, aes(colour = "black", size =1), show.legend = F ) +
geom_errorbarh(data=admay, aes(y = depth_bin, x = mean_biodensity_dm, xmin=minse, xmax=maxse, height = .2))
p4 <- p4 + geom_point(data = gmay, aes(colour = "gray", size =1), show.legend = F , position = position_nudge(y =0.2)) +
geom_errorbarh(data=gmay, position = position_nudge(y =0.2), aes(y = depth_bin, x = mean_biodensity_dm, xmin=minse, xmax=maxse, height = 0.2, color = "gray"))+
theme_bw()+
scale_color_manual(values = c("black", "gray"), labels(NULL), guides(fill=FALSE))+ ylab("")+
theme(axis.title.y=element_blank(),
axis.text.y=element_blank(),
axis.ticks.y=element_blank())
p4 <- add_sub(p4, "May", x = 0.35, hjust = 0)
p4
grid.arrange( p3, p1, p2, p4, ncol=4)
##################Season V3
library(ggplot2)
library(gridExtra)
library(cowplot)
setwd("D:/R_Workspace/SDEF/SDEF.analysis/data")
load('SDEF_roots_post_aggregation_by_season_v3.rda')
### now by biodensity
biodensity <- SDEF_roots_post_aggregation_by_season_v3
biodensity$mean_biodensity_dm <- biodensity$mean_biodensity*1000
biodensity$sd_biodensity_dm <- biodensity$sd_biodensity*1000
biodensity[is.na(biodensity)] <- 0
biodensity$se_biodensity_dm <- ((biodensity$sd_biodensity_dm)/sqrt(biodensity$n_biodensity))
biodensity$minse <- abs((biodensity$mean_biodensity_dm -biodensity$se_biodensity_dm))
biodensity$maxse <- (biodensity$mean_biodensity_dm +biodensity$se_biodensity_dm)
Espring <- subset(biodensity, biodensity$season_v3 == "Early Spring")
May <- subset(biodensity, biodensity$season_v3 == "May")
Winter <- subset(biodensity, biodensity$season_v3 == "Winter")
##############
ade <- subset(Espring, Espring$site == 'adenostoma')
ge <- subset(Espring, Espring$site == 'grass')
p1 <- ggplot(data = ade, aes(y = depth_bin, x = mean_biodensity_dm)) +
scale_y_continuous(trans = "reverse", breaks = unique(biodensity$depth_bin), labels=c("0-10", "10-20", "20-30", "30-40")) +
scale_x_continuous(position = "top", limits = c(0, .4)) + xlab("")+
geom_point(data = ade, aes(colour = "black", size =1), show.legend = F ) +
geom_errorbarh(data=ade, aes(y = depth_bin, x = mean_biodensity_dm, xmin=minse, xmax=maxse, height = .2))
p1 <- p1 + geom_point(data = ge, aes(colour = "gray", size =1), show.legend = F ,position = position_nudge(y =0.2)) +
geom_errorbarh(data=ge, position = position_nudge(y =0.2), aes(y = depth_bin, x = mean_biodensity_dm, xmin=minse, xmax=maxse, height = 0.2, color = "gray"))+
scale_color_manual(values = c("black", "gray"), labels(NULL), guides(fill=FALSE))+ theme_bw()+ ylab("Depth (cm)") +
theme(axis.title.y=element_blank(),
axis.text.y=element_blank(),
axis.ticks.y=element_blank())
p1 <- add_sub(p1, "Early Spring", x = 0.2, hjust = 0)
p1
adw <- subset(Winter, Winter$site == 'adenostoma')
gw <- subset(Winter, Winter$site == 'grass')
p3 <- ggplot(data = adw, aes(y = depth_bin, x = mean_biodensity_dm))+
scale_y_continuous(trans = "reverse", breaks = unique(biodensity$depth_bin)) +
scale_x_continuous(position = "top", limits = c(0,.4))+ xlab("") +
geom_point(data = adw, aes(colour = "black", size =1), show.legend = F ) +
geom_errorbarh(data=adw, aes(y = depth_bin, x = mean_biodensity_dm, xmin=minse, xmax=maxse, height = .2))
p3 <- p3 + geom_point(data = gw, aes(colour = "gray", size =1), show.legend = F , position = position_nudge(y =0.2)) +
geom_errorbarh(data=gw, position = position_nudge(y =0.2), aes(y = depth_bin, x = mean_biodensity_dm, xmin=minse, xmax=maxse, height = 0.2, color = "gray"))+
theme_bw()+ scale_color_manual(values = c("black", "gray"), labels(NULL), guides(fill=FALSE))+ ylab("") +
theme(axis.title.y=element_blank(),
axis.text.y=element_blank(),
axis.ticks.y=element_blank())
p3 <- add_sub(p3, "Winter", x = 0.35, hjust = 0)
p3
admay <- subset(May, May$site == 'adenostoma')
gmay <- subset(May, May$site == 'grass')
p4 <- ggplot(data = admay, aes(y = depth_bin, x = mean_biodensity_dm)) +
scale_y_continuous(trans = "reverse", breaks = unique(biodensity$depth_bin), labels=c("0-10", "10-20", "20-30", "30-40"))+
scale_x_continuous(position = "top", limits = c(0,.4))+ xlab("")+
geom_point(data = admay, aes(colour = "black", size =1), show.legend = F ) +
geom_errorbarh(data=admay, aes(y = depth_bin, x = mean_biodensity_dm, xmin=minse, xmax=maxse, height = .2))
p4 <- p4 + geom_point(data = gmay, aes(colour = "gray", size =1), show.legend = F , position = position_nudge(y =0.2)) +
geom_errorbarh(data=gmay, position = position_nudge(y =0.2), aes(y = depth_bin, x = mean_biodensity_dm, xmin=minse, xmax=maxse, height = 0.2, color = "gray"))+
theme_bw()+
scale_color_manual(values = c("black", "gray"), labels(NULL), guides(fill=FALSE))+ ylab("")+
theme(axis.title.y=element_blank(),
axis.text.y=element_blank(),
axis.ticks.y=element_blank())
p4 <- add_sub(p4, "May", x = 0.35, hjust = 0)
p4
grid.arrange( p3, p1, p4, ncol=3)
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