Oogonia per thalli

Setting up

rm(list=ls()) 
library(ggplot2)
library(ggpubr)
library(scales)
library(lubridate)

## 
## Attaching package: 'lubridate'

## The following objects are masked from 'package:base':
## 
##     date, intersect, setdiff, union

library(readr)

## 
## Attaching package: 'readr'

## The following object is masked from 'package:scales':
## 
##     col_factor

library(dplyr)

## 
## Attaching package: 'dplyr'

## The following objects are masked from 'package:stats':
## 
##     filter, lag

## The following objects are masked from 'package:base':
## 
##     intersect, setdiff, setequal, union

library(chron)

## 
## Attaching package: 'chron'

## The following objects are masked from 'package:lubridate':
## 
##     days, hours, minutes, seconds, years

library(plotly)

## 
## Attaching package: 'plotly'

## The following object is masked from 'package:ggplot2':
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##     last_plot

## The following object is masked from 'package:stats':
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##     filter

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##     layout

library(dplyr)

Data

alldata<-
  read.csv(
      "https://raw.githubusercontent.com/Cmwegener/thesis/master/data/field/CB_field_data_plus.csv",
    header = TRUE
  )
alldata$date<-as.Date(alldata$date, format = c("%Y-%m-%d"))

Subset data by site

HS<-subset(alldata, alldata$site.old == "HS")
BY<-subset(alldata, alldata$site.old == "BY")
ND<-subset(alldata, alldata$site.old == "ND")
PC<-subset(alldata, alldata$site.old == "PC")

Graph

a <-
  ggplot(data = HS,
         mapping = aes(x = date, y = oo.per.thalli, group = date)) + geom_boxplot(alpha=0.3) + ggtitle("Horseshoe Bay") +
  geom_jitter(position=position_jitter(0.5),
              size=1,
              alpha = 0.3)+ xlab("")+ylab("")+
  scale_x_date(date_breaks = "2 month", date_labels = "%b %Y") + scale_y_continuous(labels = comma) + theme(
    plot.title = element_text(size = 20, face = "plain"),
    axis.text.x = element_text(angle = 60, hjust = 1),
    axis.text = element_text(size = 20),
    axis.title = element_text(size = 20, face = "plain"),
    panel.grid.major = element_blank(),
    panel.grid.minor = element_blank(),
    panel.background = element_blank(),
    axis.line = element_line(colour = "black")
  )

b <-
  ggplot(data = BY,
         mapping = aes(x = date, y = oo.per.thalli, group = date)) + geom_boxplot(alpha=0.3) + ggtitle("Brickyard Park") +
  geom_jitter(position=position_jitter(0.5),
              size=1,
              alpha = 0.3)+xlab("")+ylab("")+
  scale_x_date(date_breaks = "2 month", date_labels = "%b %Y") + scale_y_continuous(labels = comma) + theme(
    plot.title = element_text(size = 20, face = "plain"),
    axis.text.x = element_text(angle = 60, hjust = 1),
    axis.text = element_text(size = 20),
    axis.title = element_text(size = 20, face = "plain"),
    panel.grid.major = element_blank(),
    panel.grid.minor = element_blank(),
    panel.background = element_blank(),
    axis.line = element_line(colour = "black")
  )

c <-
  ggplot(data = ND,
         mapping = aes(x = date, y = oo.per.thalli, group = date)) + geom_boxplot(alpha=0.3) + ggtitle("Point Chauncy")+
  geom_jitter(position=position_jitter(0.5),
              size=1,
              alpha = 0.3) +xlab("")+ylab("")+
  scale_x_date(date_breaks = "2 month", date_labels = "%b %Y") + scale_y_continuous(labels = comma) + theme(
    plot.title = element_text(size = 20, face = "plain"),
    axis.text.x = element_text(angle = 60, hjust = 1),
    axis.text = element_text(size = 20),
    axis.title = element_text(size = 20, face = "plain"),
    panel.grid.major = element_blank(),
    panel.grid.minor = element_blank(),
    panel.background = element_blank(),
    axis.line = element_line(colour = "black")
  )

d <-
  ggplot(data = PC,
         mapping = aes(x = date, y = oo.per.thalli, group = date)) + geom_boxplot(alpha=0.3) + ggtitle("Paradise Cay")+
  geom_jitter(position=position_jitter(0.5),
              size=1,
              alpha = 0.3)  +xlab("")+ylab("")+
  scale_x_date(date_breaks = "2 month", date_labels = "%b %Y") + scale_y_continuous(labels = comma)+ theme(
    plot.title = element_text(size = 20, face = "plain"),
    axis.text.x = element_text(angle = 60, hjust = 1),
    axis.text = element_text(size = 20),
    axis.title = element_text(size = 20, face = "plain"),
    panel.grid.major = element_blank(),
    panel.grid.minor = element_blank(),
    panel.background = element_blank(),
    axis.line = element_line(colour = "black")
  )

ooper_thallus <- ggarrange(d, c, b, a, ncol = 4, nrow = 1)

## Warning: Removed 122 rows containing non-finite values (stat_boxplot).

## Warning: Removed 122 rows containing missing values (geom_point).

## Warning: Removed 118 rows containing non-finite values (stat_boxplot).

## Warning: Removed 118 rows containing missing values (geom_point).

## Warning: Removed 116 rows containing non-finite values (stat_boxplot).

## Warning: Removed 116 rows containing missing values (geom_point).

## Warning: Removed 115 rows containing non-finite values (stat_boxplot).

## Warning: Removed 115 rows containing missing values (geom_point).

annotate_figure(
  ooper_thallus,
  left = text_grob(
    "Oogonia per thalli",
    color = "black",
    rot = 90,
    size = 25,
    face="bold"
  )
)