Generating plots of vitals for capture reports. Decent for capture reports.

vitals.R

library(readxl)
library(dplyr)
library(ggplot2)
library(gridExtra)

dat <- read_excel("CalebTest.xlsx", "temp_Vitals")

## Adding color factor for temperature plot
dat$temp[dat$Metric >= 105 & dat$VitalSign == "TR"] <- "high"
dat$temp[dat$Metric < 105 & dat$VitalSign == "TR"] <- "low"

## Testing plot
p <- ggplot(data = dat, aes(x = Interval, y = Metric)) +
  geom_point() + 
  geom_line(aes(group = factor(ndowID)))
p

## Generate split of data frame by Vital Sign (HR, TR, RR)
d <- split(dat, dat$VitalSign)

## Creating the plots
v1 <- ggplot(data = d[[1]], aes(x = Interval, y = Metric)) +
  geom_point(aes(color = factor(ndowID)), size = 4) + 
  geom_line(aes(x = Interval, y = Metric, group = factor(ndowID), color = factor(ndowID)), size = 1) +
  labs(list(title = "Animal Heart Rate", x = "Time Interval", y = "Heart Rate (beats/min)")) +
  theme_bw() +
  theme(panel.border = element_blank(),
        legend.position = "top")
v2 <- ggplot(data = d[[2]], aes(x = Interval, y = Metric)) +
  geom_point(aes(color = factor(ndowID)), size = 4) + 
  geom_line(aes(x = Interval, y = Metric, group = factor(ndowID), color = factor(ndowID)), size = 1) +
  labs(list(title = "Animal Respiratory Rate", x = "Time Interval", y = "Respiratory Rate (breaths/min)")) +
  theme_bw() +
  theme(panel.border = element_blank(),
        legend.position = "top")
v3 <- ggplot(data = d[[3]], aes(x = Interval, y = Metric)) +
  geom_point(aes(color = factor(ndowID), shape = temp), size = 4) + 
  geom_line(aes(x = Interval, y = Metric, group = factor(ndowID), color = factor(ndowID)), size = 1) +
  scale_y_continuous(breaks = seq(98, 109, 1)) + 
  labs(list(title = "Animal Temperature", x = "Time Interval", y = "Temperature (F)")) +
  theme_bw() +
  theme(panel.border = element_blank(),
        legend.position = "top")

## Multiple plots on one sheet. Not necessary.
grid.arrange(v3, v1, v2)