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3. Frequency plots.R
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3. Frequency plots.R
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#Opening Ophthalmology data on R
optho <- read.csv("June19_optho.csv")
#Checking size (no relation with stats, just checking to make sure everythng loaded properly)
object.size(optho)
print(object.size (optho), units = "Mb")
#Double checking everything is in order
length(optho$ID)
##results = 882
length(optho$Ophthalmo_AgeAtExam)
##results = 882
length(unique(optho$Ophthalmo_AgeAtExam))
##results = 40
#Seeing summary
summary(optho)
#Classification of data per column
str(optho)
# Load packages:
library(tidyverse)
library(tibble)
library(tidyr)
library(dplyr)
library(ggplot2)
library(tidytext)
library(dplyr)
library(SnowballC)
library(udpipe)
#______________________________________________
#Gives the frequency of ages
#______________________________________________
optho_ageatexam <- optho %>%
group_by(Ophthalmo_AgeAtExam) %>%
summarise(Freq = n())
optho_ageatexam
#______________________________________________
#Gives the frequency of IDs
#______________________________________________
IDFreqs <- optho %>%
group_by(ID) %>%
summarise(Freq = n())
IDFreqs
#______________________________________________
#Gives the frequency of OBD.groups
#______________________________________________
PBDFreqs <- optho %>%
group_by(PBD.group) %>%
summarise(Freq = n())
PBDFreqs
#______________________________________________
##Plotting this distribution
IDFreqsplot <- ggplot(IDFreqs, aes(y=Freq, x=ID)) +
geom_bar(stat = "identity", width=1, fill="blue")+
geom_text(aes(label=(ID)), vjust=-0.3, size=3.5)+
theme_minimal()+
coord_flip()
IDFreqsplot
##Changing Title bars
ID.Freqsplot<- IDFreqsplot + labs(title = "Frequency of IDs in sample", x = "IDs", y = "Frequency")
ID.Freqsplot
#______________________________________________
#Create diagnosis values
opthodiagnosis<-optho$Diagnosis
unique(opthodiagnosis)
#Had to seperate out the following diagnoisis manually:
#Esotropia,Nystagmus, Blindness, Retinitis pigmentosa, Optic nerve atrophy, Bilateral hyperopia, Retinal dystrophy, Optic atrophy, Amblyopia,Strabismus, Astigmatism, Maculopathy, Nyctalopia, Cystoid Macular Edema, Cataract, Conjunctivitis, Cortical visual impairement, Glaucoma, Central scotoma, Other