graph for H.pylori in Japanese

1. Total

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 ,  unknown",
                               "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",
                               "Shikata, 2008 ,  1988",
                               "Nakajima, 2010 ,  1998",
                               "Nakajima, 2010 ,  2005",
                               "Akamatsu, 2011 ,  2007",
                               "Akamatsu, 2011 ,  2008",
                               "Akamatsu, 2011 ,  2009",
                               "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, 2007  ,  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"))
data1 <- subset(data, !is.na(total))
graph1 <- ggplot(data1, aes(x = birth.year_high, 
                  y = total,
                  color = Author)) + 
  geom_line(linetype = "dashed") + 
  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("#8A2BE2", "#A52A2A", "#FFFFFF", 
                                 "#8B8878", "#66CDAA", "#CD9B1D", 
                                 "#838B8B", "#7FFF00", "#483D8B",
                                 "#0000CD", "#262626", "#CDB38B", 
                                 "#6B8E23", "#FFC1C1", "#8B8B00", 
                                 "#EE9A49", "#7EC0EE", "#8B6914", 
                                 "#104E8B", "#B4EEB4", "#EEE685", 
                                 "#FFF0F5", "#CDC1C5", "#ADD8E6", 
                                 "#68838B", "#F08080", "#00FA9A", 
                                 "#48D1CC", "#C71585", "#FF83FA", 
                                 "#36648B", "#00868B", "#8B864E", 
                                 "#D3D3D3", "#CDCDB4", "#EE4000", 
                                 "#FF83FA", "#EEE8AA", "#7CCD7C", 
                                 "#BBFFFF", "#96CDCD", "#EE0000", 
                                 "#FF3E96", "#B8860B"), 
                      limits=c("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",
                               "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, 2007  ,  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",
                               "loess"), 
                      labels = c("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",
                                 "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, 2007  ,  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",
                                 "LOWESS LINE")) + 
  ylab("Prevalence of H.pylori in Japanese (%)") + 
  xlab("Birth Year") + 
  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)
graph1

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)

library(plotly)
g <- ggplot(data=data1) +   
  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("#8A2BE2", "#A52A2A", "#FFFFFF", 
                                 "#8B8878", "#66CDAA", "#CD9B1D", 
                                 "#838B8B", "#7FFF00", "#483D8B",
                                 "#0000CD", "#262626", "#CDB38B", 
                                 "#6B8E23", "#FFC1C1", "#8B8B00", 
                                 "#EE9A49", "#7EC0EE", "#8B6914", 
                                 "#104E8B", "#B4EEB4", "#EEE685", 
                                 "#FFF0F5", "#CDC1C5", "#ADD8E6", 
                                 "#68838B", "#F08080", "#00FA9A", 
                                 "#48D1CC", "#C71585", "#FF83FA", 
                                 "#36648B", "#00868B", "#8B864E", 
                                 "#D3D3D3", "#CDCDB4", "#EE4000", 
                                 "#FF83FA", "#EEE8AA", "#7CCD7C", 
                                 "#BBFFFF", "#96CDCD", "#EE0000", 
                                 "#FF3E96", "#B8860B"), 
                      limits=c("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",
                               "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, 2007  ,  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",
                               "loess"), 
                      labels = c("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",
                                 "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, 2007  ,  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",
                                 "LOWESS LINE")) + 
  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")) 

2. 男女別

source("function for multiplot by ggplot.R")
data_sex <- subset(data, !is.na(men))

Men <- ggplot(data_sex, aes(x = birth.year_high, 
                  y = men,
                  color = Author)) + 
  geom_line(linetype = "dashed", size = 1.2) + 
  geom_point() +
  scale_x_continuous(breaks = seq(1900, 2005, 5)) + 
  scale_y_continuous(limits=c(0,100),breaks = seq(0,100,5))+
  scale_colour_manual(name = "",
                      values = c("#6495ED", "#FF8C00", 
                                 "#556B2F", "#7AC5CD", 
                                 "#458B00", "#8B7D6B", "#CD2626"), 
                      limits=c("Kikuchi, 1998 ,  1996",
                               "Ogihara, 2000 ,  1990",
                               "Yamagata, 2000 ,  1988",
                               "Kikuchi, 2005 ,  1988",
                               "Tamura, 2012 ,  2009",
                               "Hirayama, 2014 ,  2008",
                               "loess"), 
                      labels = c("Kikuchi,1998,1996",
                                 "Ogihara,2000,1990",
                                 "Yamagata,2000,1988",
                                 "Kikuchi,2005,1988",
                                 "Tamura,2012,2009",
                                 "Hirayama,2014,2008",
                                 "LOWESS LINE")) + 
  ylab("Prevalence of H.pylori in Japanese men (%)") + 
  xlab("Birth Year") + 
  geom_smooth(aes(colour = "loess"), method = "loess") + 
  theme_bw()+
  theme(legend.position = "bottom", 
        axis.text.x = element_text(size = rel(1.3)), 
        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(1.2))) 

Women <- ggplot(data_sex, aes(x = birth.year_high, 
                              y = women,
                              color = Author)) + 
  geom_line(linetype = "dashed", size = 1.2) + 
  geom_point() + 
  scale_x_continuous(breaks = seq(1900, 2005, 5)) + 
  scale_y_continuous(limits=c(0,100),breaks = seq(0,100,5))+
  scale_colour_manual(name = "",
                      values = c("#CD00CD", "#CDC9A5", 
                                 "#90EE90", "#191970", 
                                 "#668B8B", "#EE5C42", "#CD2626"), 
                      limits=c("Kikuchi, 1998 ,  1996",
                               "Ogihara, 2000 ,  1990",
                               "Yamagata, 2000 ,  1988",
                               "Kikuchi, 2005 ,  1988",
                               "Tamura, 2012 ,  2009",
                               "Hirayama, 2014 ,  2008",
                               "loess"), 
                      labels = c("Kikuchi,1998,1996",
                                 "Ogihara,2000,1990",
                                 "Yamagata,2000,1988",
                                 "Kikuchi,2005,1988",
                                 "Tamura,2012,2009",
                                 "Hirayama,2014,2008",
                                 "LOWESS LINE")) + 
  ylab("Prevalence of H.pylori in Japanese women (%)") + 
  xlab("Birth Year") + 
  geom_smooth(aes(colour = "loess"), method = "loess") + 
  theme_bw()+ 
  theme(legend.position = "bottom", 
        axis.text.x = element_text(size = rel(1.3)), 
        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(1.2)))


multiplot(Men, Women, cols = 2)