Module 7

Part 1

1. Use ggplot() to produce a histogram of salinity values

library(ggplot2)

# read in the sea temperature and salinity data
temp <- read.csv("Temperature.csv")

# histogram of salinity 
splot = ggplot(data=subset(temp, !is.na(Salinity)), aes(x = Salinity)) +
  geom_histogram(binwidth = 1, fill = "darkblue") + 
  xlab("Salinity (psu)") + ylab("Counts") + ggtitle("Distribution of Salinity Samples") 
splot

2. Make a histogram of salinity values for each year of the study, then each month

Yearly salinity distributions:

splot + facet_wrap(~ Year) + ggtitle("Distribution of Salinity Samples by Year")

Salinity distribution by year and month

splot + facet_grid(Year ~ Month) + 
  theme(axis.text.x = element_text(angle = 45, size = 5), 
        axis.text.y = element_text(size = 4)) + 
  ggtitle("Distribution of Salinity Samples", "by Month and Year")

This could also be interpreted as plot the salinity distribution for each month:

splot + facet_wrap(~ Month) + ggtitle("Distribution of Salinity Samples", "by Month")

3. Make a bloxplot of temperature values for each station

tbplot = ggplot(data = subset(temp, !is.na(Temperature)), aes(x=Station, y=Temperature)) + 
  geom_boxplot() + 
  ggtitle("Temperature Distributions by Station") + 
  theme(axis.text.x = element_text(angle = 45, size = 6))
tbplot

4. Save the last figure to a png file

ggsave("TemperatureDistributionbyStation.png", tbplot)

## Saving 7 x 5 in image

5. Reorder by mean temperature value

tbplot2 = ggplot(data = subset(temp, !is.na(Temperature)), aes(x=Station, y=Temperature)) + 
  geom_boxplot(aes(x=reorder(Station, Temperature, mean))) + 
  ggtitle("Temperature Distributions by Station") + 
  theme(axis.text.x = element_text(angle = 45, size = 6))
tbplot2

Part 2

Now make some time series plots of temperature and salinity time series. We will need a variable to represent continuous time from the start of the observations and can do this by creating a decimal date as the sum of the year and the day number / 365 (if temp is the dataframe holding the data):

temp$decdate <- temp$Year + temp$dDay3 / 365

1. Now, using this variable make a scatterplot of temperature and salinity over time

temptime = ggplot(data = subset(temp, !is.na(Temperature)), aes(x=decdate, y=Temperature, col = "Temperature")) + 
  geom_point() + geom_point(aes(y=Salinity, col = "Salinity")) +
  ylim(0, 40) + ylab("Temperature (C), Salinity (psu)") + xlab("Years") + 
  ggtitle("Temperature and Salinity of Samples over Time")
temptime

## Warning: Removed 13 rows containing missing values (`geom_point()`).

## Warning: Removed 36 rows containing missing values (`geom_point()`).

2. Make a scatterplot of salinity, grouped using facet_wrap() into different ‘Areas’

stime = ggplot(data = subset(temp, !is.na(Salinity)), 
               aes(x=decdate, y=Salinity, col = factor(Area))) + 
  facet_wrap(~ Area) + 
  xlab("Time") + ylab("Salinity (psu)") + 
  ggtitle("Salinity Samples for All Areas")
stime + geom_point()

3. Make a lineplot of salinity for each station, grouped into different ‘Areas’

stime = stime + geom_line()
stime

4. Bonus: do the same but only for area ‘OS’

First, make a subset of the data, only for the OS Area. Then repeat the above methods to plot the data. Scatterplot of temperature and salinity over time:

OSdata = subset(temp, Area == "OS")
OStempsal = ggplot(data = subset(OSdata, !is.na(Temperature)), 
                   aes(x=decdate, y=Temperature, col = "Temperature")) + 
  geom_point() + geom_point(aes(y=Salinity, col = "Salinity")) +
  ylim(0, 40) + ylab("Temperature (C), Salinity (psu)") + xlab("Years") + 
  ggtitle("Temperature and Salinity Samples for Area OS")
OStempsal

## Warning: Removed 1 rows containing missing values (`geom_point()`).

## Warning: Removed 7 rows containing missing values (`geom_point()`).

Scatterplot of salinity for Area OS:

OSstime = ggplot(data = subset(temp, !is.na(Salinity)), 
               aes(x=decdate, y=Salinity)) +
  xlab("Time") + ylab("Salinity (psu)") + ggtitle("Salinity Samples for Area OS")
OSstime + geom_point(col = "darkgrey")

Lineplot of OS salinity:

OSstime = OSstime + geom_line(col="darkgrey")
OSstime

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