Percent Reproductive Apices

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':
## 
##     last_plot

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

## The following object is masked from 'package:graphics':
## 
##     layout

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 data by site

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

Graph percent reproductive apices

a <-
  ggplot(data = HS,
         mapping = aes(x = date, y = perc.ra, group = date)) + geom_boxplot() + ggtitle("Horseshoe Bay") + theme(plot.title = element_text(size = 12, face = "plain")) +
  theme(axis.text = element_text(size = 12),
        axis.title = element_text(size = 12, face = "plain")) + ylab(" ") + xlab(" ") + theme(
          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 = perc.ra, group = date)) + geom_boxplot() +
  ylim(0, 100) + ggtitle("Brickyard Park") + theme(plot.title = element_text(size = 12, face = "plain")) +
  theme(axis.text = element_text(size = 12),
        axis.title = element_text(size = 12, face = "plain")) + ylab(" ") + xlab(" ") + theme(
          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 = perc.ra, group = date)) + geom_boxplot() + ggtitle("Point Chauncy") + theme(plot.title = element_text(size = 12, face = "plain")) +ylim(0, 100) +
  theme(axis.text = element_text(size = 12),
        axis.title = element_text(size = 12, face = "plain")) + ylab(" ") + xlab(" ") + theme(
          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 = perc.ra, group = date)) + geom_boxplot() + ggtitle("Paradise Cay") + theme(plot.title = element_text(size = 12, face = "plain")) +ylim(0, 100) +
  theme(axis.text = element_text(size = 12),
        axis.title = element_text(size = 12, face = "plain")) + ylab(" ") + xlab(" ") + theme(
          panel.grid.major = element_blank(),
          panel.grid.minor = element_blank(),
          panel.background = element_blank(),
          axis.line = element_line(colour = "black")
        )

perc.rafig <- ggarrange(d, c, b, a, ncol = 4, nrow = 1)

## Warning: Removed 39 rows containing non-finite values (stat_boxplot).

## Warning: Removed 27 rows containing non-finite values (stat_boxplot).

## Warning: Removed 13 rows containing non-finite values (stat_boxplot).

## Warning: Removed 16 rows containing non-finite values (stat_boxplot).

annotate_figure(
  perc.rafig,
  top = text_grob(
    "Percent Reproductive Apices",
    color = "black",
    face = "plain",
    size = 14
  ),
  left = text_grob(
    "Percent Reproductive Apices",
    color = "black",
    rot = 90,
    size = 12
  )
)