Manuscript revisions

Author: LockStoch

R/CTD.R

@@ -1005,3 +1005,69 @@ plot.CTD.survey.path <- function(CTD_meta, split_dates=TRUE, color_time=FALSE){
   }
   return(path_plot)
 }
+
+
+############################
+# Plot mean for CTD survey #
+############################
+CTD.plot.survey.mean <- function(CTD, survey_id,
+                                 salt_range=NULL, temp_range=NULL){
+  data <- CTD$data
+  meta <- CTD$meta
+  # Pre filter data
+  data <- data[data$survey_id %in% survey_id,]
+  
+  # aggregate data
+  data <- data[,c('depth','temperature','salinity','survey_id')]
+  data$depth <- round(data$depth)
+  if (length(survey_id) > 1){
+    data <- aggregate(data, by=list(data$depth, data$survey_id), mean)[,c(2:5)]
+    names(data)[1] <- 'survey_id'
+  } else {
+    data[,c('depth','temperature','salinity')]
+    data <- aggregate(data, by=list(data$depth), mean)[,c(2:4)]
+  }
+  
+  # Rescale salinity
+  if (!is.null(salt_range)){
+    salt_rescale <- scales::rescale(c(salt_range[1], data$salinity, salt_range[2]),
+                                    to=c(min(data$temperature),
+                                         max(data$temperature)))
+    data$salt_rescale <- salt_rescale[2:(length(salt_rescale)-1)] 
+  } else {
+    data$salt_rescale <- scales::rescale(data$salinity,
+                                         to=c(min(data$temperature), 
+                                              max(data$temperature)))
+    salt_range <- c(min(data$salinity), max(data$salinity))
+  }
+  # make title
+  if (length(survey_id) == 1){
+    title <- survey_id
+  }
+  
+
+  # Set colours
+  colors <- c("T" = "darkred", "S" = "darkgreen")
+  
+  # make the plot
+  p <- ggplot(data=data, aes(x=depth)) +
+    geom_path(aes(y=temperature,  color='T'), size=1, alpha=.8) +
+    geom_point(aes(y=temperature), size=1, alpha=.8, col='darkred') +
+    geom_path(aes(y=salt_rescale, color='S'), size=1, alpha=.8) +
+    geom_point(aes(y=salt_rescale), size=1, alpha=.8, col='darkgreen') +
+    ylab('Temperature (\u00B0C)') + xlab('Depth (m)') +
+    scale_color_manual(values = colors) + labs(color=NULL) +
+    scale_y_continuous(sec.axis = sec_axis(~scales::rescale(., to=salt_range),
+                                           name="Salinity (PSU)")) +
+    coord_flip() +
+    scale_x_reverse()
+  if (length(survey_id) > 1){
+    p <- p + facet_wrap(~survey_id)
+  }
+  
+  if (!is.null(temp_range)){
+    p <- p + ylim(temp_range)
+  }
+  
+  return(p)
+}

R/CTD_profiles.R

@@ -0,0 +1,17 @@
+# CTD profiles
+source("R/CTD.R")
+CTD <- cast.reader()
+surveys <- unique(CTD$meta$survey_id)
+CTD.plot.survey.mean(CTD, c("2015_S1"))
+CTD.plot.survey.mean(CTD, surveys) + facet_wrap(~survey_id, scales="free")
+
+# mean for all years
+mean.df <- aggregate(CTD$data[,c('temperature', 'salinity')], by=list(CTD$data$id), mean)
+# put survey back in
+mean.df$survey_id <- sapply(mean.df$Group.1, function(id) CTD$meta$survey_id[CTD$meta$file_name == id])
+
+# mean for surveys
+mean.df <- aggregate(mean.df[,c('temperature', 'salinity')], by=list(mean.df$survey_id), mean)
+names(mean.df)[1] <- 'survey_id'
+
+summary(mean.df)

R/EACpanel.R

@@ -0,0 +1,80 @@
+# make map panel
+library(rgdal)
+library(stringr)
+library(ggplot2)
+library(ggpubr)
+library(maps)
+library(sp)
+library(maptools)
+source('R/eudyptula.R')
+
+# load df.sst.EAC from bubble plot script
+
+#####################################################
+# EAC panel 2 #
+#####################################################
+# --- Data Prep --- #
+# Load in transect data
+transect.lines <- read.csv('data/transects/transect_lines.csv')
+#  stations
+stations <- read.csv('data/transects/transect_df.csv')
+moorings <- read.csv('data/surveys/moorings.csv')
+# Reshape for ggplot
+transect.lines1 <- transect.lines[,1:3]
+transect.lines2 <- transect.lines[,c(1,4,5)]
+names(transect.lines2)  <- names(transect.lines1)
+transect.lines <- rbind(transect.lines1, transect.lines2)
+# Load in coastline shapefile
+fn = './assets/shp/NSW-coastline/edited/polygon/NSW-coastline_WGS84'
+landShp <- readOGR(dsn=path.expand(str_sub(fn,1,-(nchar(basename(fn)))-1)), 
+                   layer=basename(fn))
+
+# --- Plot Map --- #
+xlim <- c(150.04, 150.33)
+ylim <- c(-36.47, -36.15)
+summary(df.sst.EAC)
+station_labels <- stations[stations$station == 1,]
+station_labels$id <- paste0("T",station_labels$transect)
+# plot
+p.panel <- ggplot() +
+  # SST
+  geom_tile(mapping=aes(x=lon, y=lat, fill=sst),
+            data=df.sst.EAC,
+            inherit.aes = F)  +
+  scale_fill_cmocean(name='thermal', limits=c(12, 28))  +
+  # transects
+  geom_line(data=transect.lines, mapping=aes(x=lon1, y=lat1, group=transect), 
+            size=.5, linetype='dashed') +
+  # stations
+  geom_point(data=stations, mapping=aes(x=lon, y=lat),
+             color='black', fill='grey', size=4, shape=21) +
+  geom_point(data=stations, mapping=aes(x=lon, y=lat),
+             color='black', size=1.5, shape=1) +
+  # moorings
+  geom_point(data=moorings, mapping=aes(x=lon, y=lat),
+             color='black', fill="green", size=4, shape=23) +
+  # coastline
+  geom_polygon(data=landShp, aes(x=long, y=lat, group=group), 
+               fill='grey', col='#636363', size=.4) +
+  # station labels
+  geom_text(data=station_labels, mapping=aes(x=lon, y=lat, label=id), size=3,
+            nudge_x=-.005, nudge_y=.008, fontface='bold') +
+  # Mooring labels
+  geom_label(data=moorings, mapping=aes(x=lon, y=lat, label=id), size=2.7, 
+             fill="green", alpha=0.4, nudge_x=0, nudge_y=-.011) +
+  # settings
+  coord_map(xlim=xlim,  ylim=ylim) +
+  theme_bw() + grids(linetype = "dashed") +
+  theme(legend.position = "none") +
+  labs(x=NULL, y=NULL, alpha=NULL, size=NULL, fill=NULL) +
+  theme(text = element_text(size=14)) +
+  theme(axis.title.x=element_blank(),
+        axis.text.x=element_blank(),
+        axis.title.y=element_blank(),
+        axis.text.y=element_blank())
+
+# Save files
+ggsave(p.panel, filename='figures/Map/panel2.png',
+       bg="transparent",dpi=300, width=2000/300, height=2000/300) 
+  
+