RG#102: Double Y axis trellis plot (weather data example)

require(latticeExtra)

require (lattice)

data(SeatacWeather)

tempatures <- xyplot(min.temp + max.temp ~ day | month,
               data = SeatacWeather, type = "l", layout = c(3, 1))
rainfall <- xyplot(precip ~ day | month, data = SeatacWeather, type = "h", lwd = 4)

doubleYScale(tempatures, rainfall, style1 = 0, style2 = 3, add.ylab2 = TRUE,
   text = c("min. T", "max. T", "rain"), columns = 3)

RG#97: Error bar plot with significance (line connecting) - publication purpose

myd <- data.frame (X = c(1:12,1:12),
                   Y = c(8, 12, 13, 18,  22, 16, 24, 29,  34, 15, 8, 6,
                         9, 10, 12, 18, 26, 28, 28, 30, 20, 10, 9, 9),
                   group = rep (c("A-group", "B-group"), each = 12),
                   error = rep (c(2.5, 3.0), each = 12))

plot1 = ggplot(data = myd, aes(x=X, y=Y, fill=group, width=0.8) ) +
     geom_errorbar(aes(ymin=Y, ymax=Y+error, width = 0.2), position=position_dodge(width=0.8)) +
     geom_bar(stat="identity", position=position_dodge(width=0.8)) +
     geom_bar(stat="identity", position=position_dodge(width=0.8), colour="black", legend=FALSE) +
     scale_fill_manual(values=c("grey70", "white")) +
     scale_x_discrete("X", limits=c(1:12)) +
     scale_y_continuous("Y (units)", expand=c(0,0), limits = c(0, 40), breaks=seq(0, 40, by=5)) + ggtitle ("My nice plot") +
     theme_bw() +
    theme( plot.title = element_text(face="bold", size=14),
          axis.title.x = element_text(face="bold", size=12),
          axis.title.y = element_text(face="bold", size=12, angle=90),
          panel.grid.major = element_blank(),
          panel.grid.minor = element_blank(),
          axis.text.y=element_text(angle=90, hjust=0.5),
          legend.title = element_blank(),
          legend.position = c(0.85,0.85),
          legend.key.size = unit(1.5, "lines"),
          legend.key = element_rect()
     )

print(plot1)

   # connecting segments
   plot1 + geom_segment(aes(x=5.7, y=16, xend=5.7, yend=28.5), col = "gray80")+
   geom_segment(aes(x=5.7, y=28.5, xend=6.1, yend=28.5), col = "gray80")      +
   geom_segment(aes(x=6.1, y=28.5, xend=6.1, yend=28), col = "gray80") +
      annotate("text", x=5.7, y=31.2, label="***")

RG#96: Basic point and line graph with error bars (publication purpose)

myd <- data.frame (X = c(1:12,1:12),
                   Y = c(8, 12, 13, 18,  22, 16, 24, 29,  34, 15, 8, 6,
                         9, 10, 12, 18, 26, 28, 28, 30, 20, 10, 9, 9),
                   group = rep (c("A-group", "B-group"), each = 12),
                   error = rep (c(2.5, 3.0), each = 12))
                   
require(ggplot2)
require(grid)
# line and point plot
f1 = ggplot(data = myd, aes(x = X, y = Y, group = group) )  # lesion becomes a classifying factor
f2 <- f1 + geom_errorbar(aes(ymin = Y - error, ymax = Y + error), width=0.3) +
geom_line() + geom_point(aes(shape=group, fill=group), size=5)

 f3 <- f2 +  scale_x_continuous("X (units)", breaks=1:12) +
     scale_y_continuous("Y (units)", limits = c(0, 40), breaks=seq(0, 40, by = 5)) +
     scale_shape_manual(values=c(24,21)) +
     scale_fill_manual(values=c("white","black")) +
     stat_abline(intercept=0, slope=0, linetype="dotted") +
     annotate("text", x=11, y=10, label="X") +
     theme_bw()

   optns <- theme (
          plot.title = element_text(face="bold", size=14),
          axis.title.x = element_text(face="bold", size=12),
          axis.title.y = element_text(face="bold", size=12, angle=90),
          panel.grid.major = element_blank(),
          panel.grid.minor = element_blank(),
          legend.position = c(0.2,0.8),
          legend.title = element_blank(),
          legend.text = element_text(size=12),
          legend.key.size = unit(1.5, "lines"),
          legend.key = element_blank()
     )
f3 +  ggtitle ( "MY awsome plot for publication") + optns

RG#76: Barplot with both X and Y quantitative value (width and height bar plot)

# data 
dff <- data.frame(x = c("Aa", "Bbb", "Ccc", "Dddd", "Eeeee"),
xvr = c(35, 50, 15, 85, 100), yvr = c(100, 75, 50, 45, 25))

# reformat data  
dff$w <- cumsum(dff$xvr)
dff$wm <- dff$w - dff$xvr
dff$wt <- with(dff, wm + (w - wm)/2)

library(ggplot2)
library(grid)

# plot 
p  <- ggplot(dff, aes(ymin = 0))
p1 <- p + geom_rect(aes(xmin = wm, xmax = w, ymax = yvr, colour = x, fill = x)) +
       scale_colour_manual(values = c("green4", "lightseagreen", "pink", "blue3", "tan")) +
        scale_fill_manual (values = c("green4", "lightseagreen", "pink", "blue3", "tan"))
       

p1 + geom_text(aes(x = wt, y = yvr * 0.8, label = x)) +
     theme_bw() + labs(x = NULL, y = NULL) +
     theme(axis.ticks = element_blank(),axis.text.x = element_blank(),     axis.text.y = element_blank(), legend.position = "none") +
     annotate("text", x = 120, y = 83, label = "Bbb") +
     annotate("text", x = 270, y = 35, label = "Eeeee") +
     geom_segment(aes(x = 100, y = 80, xend = 80, yend = 75),
     arrow = arrow(length = unit(0.5, "cm"))) +
         geom_segment(aes(x = 280, y = 32, xend = 250, yend = 25),
     arrow = arrow(length = unit(0.5, "cm"))) + theme_bw()