Grammar of Graphics for base plot

In plotbb: Grammar of Graphics for 'base' Plot

knitr::opts_chunk$set(tidy = FALSE,
           message = FALSE)

library(dplyr)
library(plotbb) 

library(dplyr)
library(plotbb) 

Aesthetic mapping

bb_aes() for aesthetic mapping, that equivalents to ggplot2::aes().

library(plotbb)

p <- bbplot(mtcars, bb_aes(mpg, disp, col=factor(cyl)))
p + bb_grid(col='grey50', lty='dashed') + bb_point(pch=19) 

Geometric layer

p2 <- p + bb_point() + bb_lm(bb_aes(group=cyl), lwd=2)
p3 <- p2 + bb_lm(col="red", lwd=3, lty='dotted')
p4 <- p + bb_text(bb_aes(label=cyl), cex=2)
## oldpar <- par()$mfrow
## par(mfrow=c(1,3))
## p2; p3; p4
## par(mfrow=oldpar)
aplot::plot_list(p2, p3, p4, ncol=3, tag_levels = 'A')

Heatmap

df <- data.frame(x = rep(1:10, 12),
                 y = rep(1:12, each = 10),
                 values = rnorm(120, mean = 10, sd = 5),
                 type = sample(LETTERS[1:5], 120, replace=TRUE),
                 stringsAsFactors = FALSE)

h1 <- bbplot(df, bb_aes(x,y, col=values)) + bb_tile() + 
  bb_title("heatmap for continuous numerical values") 
h2 <- bbplot(df, bb_aes(x,y, col=values)) + bb_tile() + bb_scale_col_palette("YlOrRd") +
  bb_title("applying a color palette") 
h3 <- bbplot(df, bb_aes(x,y, col=type)) + bb_tile() +
  bb_title("heatmap for discrete categorical values") 
h4 <- bbplot(df, bb_aes(x,y, col=values)) + bb_tile() + bb_text(col='black') +
  bb_title("heatmap with text labels") + bb_theme_expand()
aplot::plot_list(h1, h2, h3, h4, ncol=2, tag_levels = 'A')

TODO

• [x] bb_grid
• [x] bb_point
• [x] bb_lm
• [x] bb_text
• [x] bb_tile
• more layers need to be added

Setting labels

p2 + bb_labs(title = "hello", sub = "just for demo",
              xlab="this is xlab", ylab = "this is ylab") +
  bb_title("hello world") # last one rules

Theme

g <- p2 +
     bb_theme(col.main="red", cex.main=2,
             mar = c(4, 4, 3, 1)) +
     bb_title("applying graphics::par")
g2 <- p2 + bb_title("theme has no side effect")
aplot::plot_list(g, g2, ncol=2, tag_levels = 'A')

bb_theme has no side effect and will only apply to the bbplot object that it added to. This is very important for developing pre-defined themes.

p4 <- p3 + bb_theme_expand()
aplot::plot_list(p4, p3, ncol=2, tag_levels = 'A')

p + bb_grid(col='grey50', lty='dashed') +
  bb_point(pch=19) +
  bb_theme_expand() +
  bb_theme_grey() 

p + bb_point(pch=19, cex=2) +
  bb_theme_expand() +
  bb_theme_deepblue() 

TODO

• [x] bb_theme_expand
• [x] bb_theme_grey
• [x] bb_theme_deepblue
• develop more pre-defined themes

Scale

• [x] bb_scale_col_palette
• more to be implemented

Legend

Not yet implemented

Using existing code with plotbb

Suppose we have existing code to plot something:

plot(mtcars$mpg, mtcars$disp)
abline(lm(disp ~ mpg, data=mtcars), col='red')

We can wrap the codes into a function:

f <- function() { 
  plot(mtcars$mpg, mtcars$disp)
  abline(lm(disp ~ mpg, data=mtcars), col='red')
}

Then we can convert it to a bbplot object. The plot produced by the function will be used as the canvas, and we can apply theme and add layers to it:

library(dplyr) 
d <- group_by(mtcars, cyl) %>%
  summarize(xm=mean(mpg), ym=mean(disp))

pp <- as.bbplot(f) +
   bb_theme_expand() +
   bb_theme_grey() +
   bb_lm(bb_aes(mpg, disp, group=cyl, col=factor(cyl)), data=mtcars, lwd=2, lty='dashed') +
   bb_point(bb_aes(xm, ym, col=factor(cyl)), data=d, pch=19, cex=2) +
   bb_title("hello plotbb") +
   bb_grid(col='grey30', lty='dashed') ## grid lines were plotted as background by default

As there are many features currently not available, plotbb supports adding layers using base graphics commands that you are already familiar with. Any base graphics commands in formula, expression or function can be served as layer to be added to a bbplot object.

pp + (~points(30, 400, pch=19, col="red", cex=3)) + 
   ~text(30, 420, label="hae fun :)", col="blue", cex=1.2)

Here is another example to use plotbb with the ape package to visualize phylogenetic tree.

require(ape)
set.seed(2020-09-10)
x = rtree(10)

p = as.bbplot(
  function() 
    plot(x, cex=2, edge.width=2, 
        edge.color="white", tip.color='purple')
  )

p + bb_theme_expand() + bb_theme_deepblue() +
  (~nodelabels(node = 14, pie = matrix(rep(1, 4), 1), cex = 2)) +
  (~nodelabels(node = 15, pie = matrix(rep(1, 3), 1), cex = 2)) +
  (~nodelabels(node = 18, pie = matrix(rep(1, 5), 1), cex = 2)) +
  bb_labs(title = 'phylogenetic tree plotted by base graphics') +
  bb_theme(col.main = "firebrick", cex.main=2)

plotbb documentation built on Sept. 8, 2021, 9:07 a.m.