In [1]:

    

library(gdata)
library(ggplot2)
library(grid)
library(gridExtra)


    

    




gdata: read.xls support for 'XLS' (Excel 97-2004) files ENABLED.

gdata: read.xls support for 'XLSX' (Excel 2007+) files ENABLED.

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In [3]:

    

source("C.2.5- Within_regions_generic_plot.R")


    

In [4]:

    

DT <- read.table("../Data/All_data.txt")
ratio_align <- read.table("../Data/Alignment_ratios_within_regions_across_diseases_wt_sims_patients_metrs_burdens.txt")


    

In [5]:

    

DT$Dis_lab <- DT$Disease
levels(DT$Dis_lab)


    

    






	
'All'
	
'Cardiovascular and circulatory diseases'
	
'Chronic respiratory diseases'
	
'Cirrhosis of the liver'
	
'Congenital anomalies'
	
'Diabetes, urinary diseases and male infertility'
	
'Diarrhea, lower respiratory infections, meningitis, and other common infectious diseases'
	
'Digestive diseases (except cirrhosis)'
	
'Gynecological diseases'
	
'Hemoglobinopathies and hemolytic anemias'
	
'Hepatitis'
	
'HIV/AIDS'
	
'Leprosy'
	
'Malaria'
	
'Maternal disorders'
	
'Mental and behavioral disorders'
	
'Musculoskeletal disorders'
	
'Neglected tropical diseases excluding malaria'
	
'Neonatal disorders'
	
'Neoplasms'
	
'Neurological disorders'
	
'Nutritional deficiencies'
	
'Oral disorders'
	
'Sense organ diseases'
	
'Sexually transmitted diseases excluding HIV'
	
'Skin and subcutaneous diseases'
	
'Sudden infant death syndrome'
	
'Tuberculosis'

In [6]:

    

#Disease labels for plot
levels(DT$Dis_lab) <- c("",
               "Cardiovasc.\nand circulatory",
               "Chronic\nrespiratory",
               "Cirrhosis",
               "Congenital\nanomalies",
               "Diabetes, urinary\nmale infertility",
               "Common\ninfect. dis.",
               "Digestive",
               "Gynecol.",
               "Hemoglob. and\nhemolytic anemia",
               "Hepatitis",
               "HIV",
               "Leprosy",
               "Malaria",
               "Maternal\ndisorders",
               "Mental and\nbehavioral",
               "Musculosk.",
               "Neglected trop.",
               "Neonatal\ndisorders",
               "Neoplasms",
               "Neurological",
               "Nutritional",
               "Oral",
               "Sense organ",
               "STD",
               "Skin and\nsubcutaneous",
               "Sudden infant death",
               "Tuberculosis")


    

In [7]:

    

#Region labels
DT$regs_lab <- DT$Region
levels(DT$regs_lab)


    

    






	
'All'
	
'Central Europe, Eastern Europe, and Central Asia'
	
'High-income'
	
'Latin America and Caribbean'
	
'Non-HI'
	
'North Africa and Middle East'
	
'South Asia'
	
'Southeast Asia, East Asia and Oceania'
	
'Sub-Saharian Africa'

In [8]:

    

levels(DT$regs_lab) <-  c("World",
                          "Eastern Europe and Central Asia",
                          "High-income countries",
                          "Latin America and Caribbean",
                          "Non-high-income countries",
                          "North Africa and Middle East",
                          "South Asia",
                          "Southeast Asia, East Asia and Oceania",
                          "Sub-Saharian Africa")


    

In [9]:

    

L <- Within_2Regions_plot(metr_burden = "yld",metr_res = "RCTs",region1 = "High-income",region2="Sub-Saharian Africa")


    

In [10]:

    

options(repr.plot.width=10, repr.plot.height=5)
grid.arrange(L[[1]],L[[2]], ncol=2)


    

In [12]:

    

options(repr.plot.width=5, repr.plot.height=5)
Within_Region_plot(metr_burden = "yld",metr_res = "Patients",region = "South Asia")


    

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