ggplot tricks

ggplot_help.R

# ggplot2 implements the idea of a "grammar of graphics". The grammar implemented 
#   by ggplot2 could be summarized as follows:
#
#   plot: coord, scale, facet(?) + layers
#   layer: data mapping stat geom position?
#
# A plot is defined by a coordinate system (coord), one or more scales (scale), an
#   optional faceting specification (facet), and one or more layers (layer). A layer
#   is defined as an R data frame (data), a specification mapping columns of that 
#   frame into aesthetic properties (mapping), a statistical approach to summarize 
#   the rows of that frame (stat), a geometric object to visually represent that 
#   summary (geom), and an optional position adjustment to move overlapping 
#   geometric objects out of their way (position).
#
# axes: breaks & minor breaks are "ticks"
#       limits
#       name: axis title

# geom_bar(aes(order = desc(cut)))


ggplot(df.topotu, aes(x=OTU, y=prop * 100, fill=core) ) + geom_point() +
  xlab(paste("Top", n, "OTUs in rank order")) +
  ylab("percent abundance") +
  ylim(0, 100) +
  xlim(1, 1000)

geom_histogram(mapping = NULL, data = NULL, stat = "bin", position = "stack", ...)

geom_histogram(binwidth = 1)   # freq
geom_histogram(aes(weight = votes)) # count

geom_bar()

w <- ggplot(diamonds, aes(clarity, fill = cut))
w + geom_bar()
# ORDER
w + geom_bar(aes(order = desc(cut))) # order factors in descending order
ggplot(diamonds, aes(clarity, fill = cut, order = -as.numeric(cut))) +
+     geom_bar()


geom_point()
geom_jitter()


geom_line()
geom_line(aes(group = Subject)) # The group aesthetic maps a different line for each subject

library(nlme)
ggplot(Oxboys, aes(age, height, color= Subject)) +
geom_point(size = 1) +
geom_smooth(aes(group = Subject, color = Subject), method = "lm", se = FALSE)


geom_abline() # draws a line defined by slope and y-axis intercept.

geom_boxplot(mepping, data, stat = "boxplot", 
    outlier.colour = "black", outlier.shape = 16, outlier.size = 2, 
    notch = FALSE, notchwidth = 0.5, ...)
  # http://docs.ggplot2.org/0.9.3.1/geom_boxplot.html
  # remember that the x axis must be discrete/factor
geom_boxplot(aes(fill = factor(cyl)))  # colors box
geom_boxplot(aes(color = factor(cyl))) # colors lines of box & whiskers
geom_boxplot(outlier.shape=3, outlier.size=1 ) # outlier sm. crosses
geom_boxplot() + coord_flip() # horizontal 


geom_ribbon(aes(ymin=mean-sd, ymax=mean+sd), fill= "grey70")


#######################################
# scale axes

# set ticks
scale_y_log10(breaks=c(0.01, 0.1, 1, 10)) 

########################################
# facets

facet_grid(facets, margins = FALSE, scales = "fixed", space = "fixed", shrink = TRUE, 
  labeller = "label_value", as.table = TRUE, drop = TRUE)


facet_wrap(facets, nrow = NULL, ncol = NULL, scales = "fixed", shrink = TRUE, as.table = TRUE, 
  drop = TRUE)

########################################
# theme()

# rotate axis labels
theme(axis.text.x = element_text(angle = 90, hjust = 1)) +

# no axis labels
theme(axis.text.y = element_blank())  

# https://github.com/hadley/ggplot2/wiki/Legend-Attributes

theme()
# http://docs.ggplot2.org/current/theme.html

axis.title = element_blank()
strip.text = element_text(size=18)

axis.line = theme_blank(), 
axis.text.x = theme_blank(), 
axis.text.y = theme_blank(),
axis.ticks = theme_blank(), 
axis.title.x = theme_blank(), 
axis.title.y = theme_blank(), 
axis.ticks.length = unit(0, "lines"), 
axis.ticks.margin = unit(0, "lines"), 

legend.text = element_text(size = 12)
legend.title = element_text(size = 14)
legend.position = "none"

melt_help.R

df.a <- melt(df.otu, 
          id.vars="OTU",   # cols to keep
          variable.name="samples",  # colname variables (colnames in wide)
          value.name="prop" # colname for values)