Average oogonia per conceptacle

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':
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##     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'

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##     last_plot

## The following object is masked from 'package:stats':
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library(dplyr)

Setting up 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

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 = oog.per.con, group = date)) + geom_boxplot() +
  ggtitle("Horseshoe Bay") + ylim(0, 150) +
  theme(
    plot.title = element_text(size = 12, face = "plain"),
    axis.text.x = element_text(angle = 60, hjust = 1),
    axis.text = element_text(size = 12),
    axis.title = element_text(size = 12, 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 = oog.per.con, group = date)) + geom_boxplot() + ggtitle("Brickyard Park") +
  ylim(0, 150) + theme(
    plot.title = element_text(size = 12, face = "plain"),
    axis.text.x = element_text(angle = 60, hjust = 1),
    axis.text = element_text(size = 12),
    axis.title = element_text(size = 12, 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 = oog.per.con, group = date)) + geom_boxplot() + ggtitle("Point Chauncy") +
  ylim(0, 150) + theme(
    plot.title = element_text(size = 12, face = "plain"),
    axis.text.x = element_text(angle = 60, hjust = 1),
    axis.text = element_text(size = 12),
    axis.title = element_text(size = 12, 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 = oog.per.con, group = date)) + geom_boxplot() + ggtitle("Paradise Cay") +
  ylim(0, 150) + theme(plot.title = element_text(size = 12, face = "plain")) +
  theme(
    plot.title = element_text(size = 12, face = "plain"),
    axis.text.x = element_text(angle = 60, hjust = 1),
    axis.text = element_text(size = 12),
    axis.title = element_text(size = 12, face = "plain"),
    panel.grid.major = element_blank(),
    panel.grid.minor = element_blank(),
    panel.background = element_blank(),
    axis.line = element_line(colour = "black")
  )

Stack and annotate

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

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

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

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

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

annotate_figure(oopercfigure,
                top = text_grob("Oogonia per conceptacle", color = "black", face = "plain", size = 14), left = text_grob("Number of oogonia per conceptacle", color = "black", rot = 90, size=12))