Graph 1 H.pylori prevalence in Japanese

In men and women combined:

data <- read.csv("dataforpylorigraph.csv", header = TRUE)
library(ggplot2)
library(grid)
data$birth.year_high <- as.numeric(data$birth.year_high)
#summary(data$birth.year_high)
data$total <- as.numeric(data$total)
#summary(data$total)
data$Author <- paste(data$Author..year.of.publication, ", ", 
                     data$Research.Year)
data$Study.No <- factor(data$Study.No, ordered = TRUE)
data$Author <- factor(data$Author,
                      levels=c("Asaka, 1992 ,  1990",
                               "Kikuchi, 1998 ,  1996",
                               "Fujisawa, 1999 ,  1974",
                               "Fujisawa, 1999 ,  1984",
                               "Fujisawa, 1999 ,  1994",
                               "Ogihara, 2000 ,  1990",
                               "Yamagata, 2000 ,  1988",
                               "Kurosawa, 2000 ,  1995",
                               "Yamashita, 2001 ,  1995",
                               "Fukuda, 2001 ,  1986",
                               "Fukuda, 2001 ,  1998",
                               "Kinjo, 2002 ,  2000",
                               "Kato, 2003 ,  2003",
                               "Kato, 2004 ,  2004",
                               "Kikuchi, 2005 ,  1988",
                               "Kawade, 2005 ,  2000",
                               "Sasazuki, 2006 ,  1990",
                               "Nakajima, 2010 ,  1998",
                               "Nakajima, 2010 ,  2005",
                               "Akamatsu, 2011 ,  2007",
                               "Akamatsu, 2011 ,  2008",
                               "Akamatsu, 2011 ,  2009",
                               "Akamatsu, 2015 ,  2010",
                               "Akamatsu, 2015 ,  2011",
                               "Akamatsu, 2015 ,  2012",
                               "Akamatsu, 2015 ,  2013",
                               "Toyoda, 2012 ,  2005",
                               "Tamura, 2012 ,  2009",
                               "Kikuchi, 2013 ,  1997",
                               "Kikuchi, 2013 ,  2003",
                               "Urita, 2013 ,  2002",
                               "Ueda, 2014 ,  2005",
                               "Hirayama, 2014 ,  2008",
                               "Okuda, 2014 ,  2010",
                               "Watanabe, 2015 ,  2010" ,
                               "Kamada, 2015 ,  2011",
                               "Shiotani, 2008 ,  2005",
                               "Yamaji, 2001 ,  1997", 
                               "Shibata, 2002 ,  1993",
                               "Youn, 1998 ,  1993", 
                               "Naito, 2008 ,  2002",
                               "Naito, 2008 ,  2003",
                               "Shimatani, 2005 ,  2000",
                               "Nobuta, 2004 ,  1996",
                               "Kumagai, 1998 ,  1986",
                               "Kumagai, 1998 ,  1994",
                               "Reploge, 1996 ,  1980",
                               "Fukao, 1993 ,  1985",
                               "Shimoyama 2012 ,  2005",
                               "Shimoyama 2014 ,  2012",
                               "Nakao 2011 ,  2003",
                               "Kawai 2010 ,  2004",
                               "Fujimoto 2007 ,  2002"))
data1 <- subset(data, !is.na(total))
ytitle <- expression(paste("Prevalence of ", italic("H.pylori"), " in Japanese (%)"))
graph1 <- ggplot(data1, aes(x = birth.year_high, 
                  y = total,
                  color = Author, size = n_total)) + 
  geom_line(size = 0.8) + 
  geom_point() + 
  scale_x_continuous(breaks = seq(1900, 2005, 5)) + 
  scale_y_continuous(breaks = seq(0,100,5)) +
  scale_colour_manual(name = "Author,\nPublish year,\nStudy year",
                      values = c("#CDC0B0", "#8B8378", "#7FFFD4", "#66CDAA", "#458B74", "#C1CDCD", "#838B8B", "#FFE4C4", "#CDB79E", "#8B7D6B", "#000000", "#0000FF", "#00008B", "#8A2BE2", "#A52A2A", "#FF4040", "#DEB887", "#5F9EA0", "#8EE5EE", "#53868B", "#7FFF00", "#458B00", "#D2691E", "#8B4513", "#EE6A50", "#8B3E2F", "#6495ED", "#8B8878", "#9A32CD", "#9BCD9B", "#DAA520", "#00688B", "#228B22", "#FF69B4", "#8B3A62", "#8DB6CD", "#CD8162", "#8B5F65", "#CD00CD", "#48D1CC", "#000080", "#6B8E23", "#8B2500", "#27408B", "#CD7054", "#8B8682", "#EE7942", "#8B8B00", "#FFFF00", "#EE82EE", "#C6E2FF", "#303030", "#6E7B8B", 
                                "#D2691E"), 
                      limits=c("Asaka, 1992 ,  1990",
                               "Kikuchi, 1998 ,  1996",
                               "Fujisawa, 1999 ,  1974",
                               "Fujisawa, 1999 ,  1984",
                               "Fujisawa, 1999 ,  1994",
                               "Ogihara, 2000 ,  1990",
                               "Yamagata, 2000 ,  1988",
                               "Kurosawa, 2000 ,  1995",
                               "Yamashita, 2001 ,  1995",
                               "Fukuda, 2001 ,  1986",
                               "Fukuda, 2001 ,  1998",
                               "Kinjo, 2002 ,  2000",
                               "Kato, 2003 ,  2003",
                               "Kato, 2004 ,  2004",
                               "Kikuchi, 2005 ,  1988",
                               "Kawade, 2005 ,  2000",
                               "Sasazuki, 2006 ,  1990",
                               "Nakajima, 2010 ,  1998",
                               "Nakajima, 2010 ,  2005",
                               "Akamatsu, 2011 ,  2007",
                               "Akamatsu, 2011 ,  2008",
                               "Akamatsu, 2011 ,  2009",
                               "Akamatsu, 2015 ,  2010",
                               "Akamatsu, 2015 ,  2011",
                               "Akamatsu, 2015 ,  2012",
                               "Akamatsu, 2015 ,  2013",
                               "Toyoda, 2012 ,  2005",
                               "Tamura, 2012 ,  2009",
                               "Kikuchi, 2013 ,  1997",
                               "Kikuchi, 2013 ,  2003",
                               "Urita, 2013 ,  2002",
                               "Ueda, 2014 ,  2005",
                               "Hirayama, 2014 ,  2008",
                               "Okuda, 2014 ,  2010",
                               "Watanabe, 2015 ,  2010" ,
                               "Kamada, 2015 ,  2011",
                               "Shiotani, 2008 ,  2005",
                               "Yamaji, 2001 ,  1997", 
                               "Shibata, 2002 ,  1993",
                               "Youn, 1998 ,  1993", 
                               "Naito, 2008 ,  2002",
                               "Naito, 2008 ,  2003",
                               "Shimatani, 2005 ,  2000",
                               "Nobuta, 2004 ,  1996",
                               "Kumagai, 1998 ,  1986",
                               "Kumagai, 1998 ,  1994",
                               "Reploge, 1996 ,  1980",
                               "Fukao, 1993 ,  1985",
                               "Shimoyama 2012 ,  2005",
                               "Shimoyama 2014 ,  2012",
                               "Nakao 2011 ,  2003",
                               "Kawai 2010 ,  2004",
                               "Fujimoto 2007 ,  2002",
                               "loess"), 
                      labels = c("Asaka,1992,1990",
                                 "Kikuchi,1998,1996",
                                 "Fujisawa,1999,1974",
                                 "Fujisawa,1999,1984",
                                 "Fujisawa,1999,1994",
                                 "Ogihara,2000,1990",
                                 "Yamagata,2000,1988",
                                 "Kurosawa,2000,1995",
                                 "Yamashita,2001,1995",
                                 "Fukuda,2001,1986",
                                 "Fukuda,2001,1998",
                                 "Kinjo,2002,2000",
                                 "Kato,2003,2003",
                                 "Kato,2004,2004",
                                 "Kikuchi,2005,1988",
                                 "Kawade,2005,2000",
                                 "Sasazuki,2006,1990",
                                 "Nakajima,2010,1998",
                                 "Nakajima,2010,2005",
                                 "Akamatsu,2011,2007",
                                 "Akamatsu,2011,2008",
                                 "Akamatsu,2011,2009",
                                 "Akamatsu,2011,2010",
                                 "Akamatsu,2011,2011",
                                 "Akamatsu,2011,2012",
                                 "Akamatsu,2011,2013",
                                 "Toyoda,2012,2005",
                                 "Tamura,2012,2009",
                                 "Kikuchi,2013,1997",
                                 "Kikuchi,2013,2003",
                                 "Urita,2013,2002",
                                 "Ueda,2014,2005",
                                 "Hirayama,2014,2008",
                                 "Okuda,2014,2010",
                                 "Watanabe,2015,2010" ,
                                 "Kamada,2015,2011", 
                                 "Shiotani,2008,2005",
                                 "Yamaji,2001,1997", 
                                 "Shibata,2002,1993",
                                 "Youn,1998,1993", 
                                 "Naito,2008,2002",
                                 "Naito,2008,2003",
                                 "Shimatani,2005,2000",
                                 "Nobuta,2004,1996",
                                 "Kumagai,1998,1986",
                                 "Kumagai,1998,1994",
                                 "Reploge,1996,1980",
                                 "Fukao,1993,1985",
                                 "Shimoyama,2012,2005",
                                 "Shimoyama,2014,2012",
                                 "Nakao,2011,2003",
                                 "Kawai,2010,2004",
                                 "Fujimoto,2007,2002",
                                 "TOTAL")) + 
  labs(x = "Birth Year", 
       y = ytitle) + 
  geom_smooth(aes(colour = "loess"), method = "loess") + 
  theme_bw() +   
  theme(legend.position = "bottom", 
        axis.text.x = element_text(size = rel(1.5)), 
        axis.text.y = element_text(size = rel(1.5)), 
        axis.title.x = element_text(size = rel(1.5)), 
        axis.title.y = element_text(size = rel(1.5)), 
        legend.text = element_text(size = rel(1.1)), 
        legend.title = element_text(size = rel(1.1))) + 
  annotate("segment", x = 1929, xend = 1938.4,
           y = 20.36, yend = 44.36,
           colour = "red", size = 1.2,
           arrow=arrow(length = unit(0.15,"inches"))) + 
  annotate("segment", x = 1919, xend = 1928.4, 
           y = 40.3, yend = 51.3, 
           colour = "red", size = 1.2, 
           arrow = arrow(length = unit(0.15, "inches"))) + 
  annotate("text", x=1929, y=19, label = "Ueda, 2014, 2005",
           fontface = "italic", size = 5) + 
  annotate("text", x=1919, y=39, label = "Watanabe, 2015, 2010",
           fontface = "italic", size = 5) + theme(axis.line = element_line(colour = "bisque4", 
    size = 2, linetype = "solid"), panel.grid.major = element_line(colour = "lightsteelblue", 
    linetype = "dashed"), axis.text = element_text(size = 12, 
    face = "bold", colour = "gray0")) +labs(x = "Birth Year (from 1906 to 2003)") + theme(legend.text = element_text(size = 11, 
    colour = "darkblue"), legend.title = element_text(face = "bold"), 
    legend.key = element_rect(fill = NA, 
        colour = NA), legend.background = element_rect(fill = "whitesmoke", 
        size = 1), legend.direction = "horizontal") + 
  guides(size = guide_legend("Sample size"))
graph1

Bubble graph with 40 papers:

require(rCharts)
h1 <- hPlot(x = "birth.year_high", y = "total",
            data = data1,
            type = c("bubble"), #"spline"
            group = c("Author"),
            size = "n_total"
       )
h1$title(text = "Prevalence of <i>H.pylori</i> in Japanese", align = "center")
h1$chart(zoomType = "xy")
h1$yAxis(min=0, max = 100, 
         title = list(text = "Persentage (%)"), tickInterval= 10, 
         scalable = TRUE)
h1$xAxis(title = list(text = "Birth year (1906 - 2003)")) #, 
         #formatter = "function () {
         #return Highcharts.numberFormat(this.value, 0, '', '');} // Remove the thousands sep?")
h1$legend(title = list(text = "Author, publish year, study year"))
#h1$series(name = "LOWESS LINE", regression = TRUE, type = "loess")
h1$set(height = 700)
h1$exporting(enabled = T)
h1$show('inline', include_assets = TRUE, standalone = TRUE)

5 papers directly reported prevalences by birth cohorts:

data$birth_year_data <- as.logical(data$birth_year_data)
data_birth <- subset(data, birth_year_data == TRUE)
data_birth$Author <- droplevels(data_birth$Author)
library(plotly)
g <- ggplot(data=data_birth) +   
  geom_point(mapping=aes(x = birth.year_high,
                         y = total, colour = Author, 
                         size = n_total)) +  
  geom_line(mapping = aes(x = birth.year_high, 
                          y = total, colour = Author), linetype = "dashed") + 
  scale_x_continuous(breaks = seq(1900, 2005, 5)) + 
  scale_y_continuous(breaks = seq(0,100,5)) +
  scale_colour_manual(name = "Author,\nPublish year,\nStudy year",
                      values = c("#104E8B", "#CD9B1D", "#8B008B", "#FF69B4", "#48D1CC", "#8B8B00"), 
                      limits=c("Ueda, 2014 ,  2005",
                               "Watanabe, 2015 ,  2010",
                               "Shimatani, 2005 ,  2000",
                               "Reploge, 1996 ,  1980",
                               "Shimoyama 2012 ,  2005",
                               "loess"), 
                      labels = c("Ueda,2014,2005",
                               "Watanabe,2015,2010",
                               "Shimatani,2005,2000",
                               "Reploge,1996,1980",
                               "Shimoyama,2012,2005",
                               "TOTAL")) + 
  ylab("Prevalence of <i>H.pylori</i> in Japanese (%)") + 
  xlab("Birth Year") + 
  geom_smooth(mapping = aes(x = birth.year_high, 
                            y = total,colour = "loess"), method = "loess") + 
  theme_bw() +
  theme(               legend.position="none",
                       axis.text.x = element_text(size = rel(1.3)), 
                       axis.text.y = element_text(size = rel(1.3)), 
                       axis.title.x = element_text(size = rel(1.5)), 
                       axis.title.y = element_text(size = rel(1.3)))
#ggplotly(g)
layout(ggplotly(g), legend=list(orientation = "h"))