Ggplot2

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ggplot2

Books

Tutorials

Some examples

Examples from 'R for Data Science' book - Aesthetic mappings

ggplot(data = mpg) + 
  geom_point(mapping = aes(x = displ, y = hwy))
  # the 'mapping' is the 1st argument for all geom_* functions, so we can safely skip it.
# template
ggplot(data = <DATA>) + 
  <GEOM_FUNCTION>(mapping = aes(<MAPPINGS>))

# add another variable through color, size, alpha or shape
ggplot(data = mpg) + 
  geom_point(aes(x = displ, y = hwy, color = class))

ggplot(data = mpg) + 
  geom_point(aes(x = displ, y = hwy, size = class))

ggplot(data = mpg) + 
  geom_point(aes(x = displ, y = hwy, alpha = class))

ggplot(data = mpg) + 
  geom_point(aes(x = displ, y = hwy, shape = class))

ggplot(data = mpg) + 
  geom_point(aes(x = displ, y = hwy), color = "blue")

# add another variable through facets
ggplot(data = mpg) + 
  geom_point(aes(x = displ, y = hwy)) + 
  facet_wrap(~ class, nrow = 2)

# add another 2 variables through facets
ggplot(data = mpg) + 
  geom_point(aes(x = displ, y = hwy)) + 
  facet_grid(drv ~ cyl)

Examples from 'R for Data Science' book - Geometric objects

# Points
ggplot(data = mpg) + 
  geom_point(aes(x = displ, y = hwy))

# Smoothed
ggplot(data = mpg) + 
  geom_smooth(aes(x = displ, y = hwy))

# Points + smoother
ggplot(data = mpg) + 
  geom_point(aes(x = displ, y = hwy)) +
  geom_smooth(aes(x = displ, y = hwy))

# Colored points + smoother
ggplot(data = mpg, aes(x = displ, y = hwy)) + 
  geom_point(aes(color = class)) + 
  geom_smooth()

Examples from 'R for Data Science' book - Transformation

# y axis = counts
# bar plot
ggplot(data = diamonds) + 
  geom_bar(aes(x = cut))
# Or
ggplot(data = diamonds) + 
  stat_count(aes(x = cut))

# y axis = proportion
ggplot(data = diamonds) + 
  geom_bar(aes(x = cut, y = ..prop.., group = 1))

# bar plot with 2 variables
ggplot(data = diamonds) + 
  geom_bar(aes(x = cut, fill = clarity))

facet_wrap and facet_grid to create a panel of plots

Color palette

scales packages - ggplot2 default color palette

Emulate ggplot2 default color palette

Answer 1 

gg_color_hue <- function(n) {
  hues = seq(15, 375, length = n + 1)
  hcl(h = hues, l = 65, c = 100)[1:n]
}

n = 4
cols = gg_color_hue(n)

dev.new(width = 4, height = 4)
plot(1:n, pch = 16, cex = 2, col = cols)

Answer 2 (better, it shows the color values in HEX). It should be read from left to right and then top to down.

scales package 

library(scales)
show_col(hue_pal()(4))

Class variables

"Set1" is a good choice. See RColorBrewer::display.brewer.all()

Heatmap for single channel

https://scales.r-lib.org/ 

# White <----> Blue
RColorBrewer::display.brewer.pal(n = 8, name = "Blues")

Heatmap for dual channels

http://www.sthda.com/english/wiki/colors-in-r 

library(RcolorBrewer)
# Red <----> Blue
display.brewer.pal(n = 8, name = 'RdBu')
# Hexadecimal color specification 
brewer.pal(n = 8, name = "RdBu")

plot(1:8, col=brewer_pal(palette = "RdBu")(8), pch=20, cex=4)

# Blue <----> Red
plot(1:8, col=rev(brewer_pal(palette = "RdBu")(8)), pch=20, cex=4)

Twopalette.svg

Themes and background for ggplot2

Common plots

Line plots

Boxplot with jittering

# df2 is n x 2 
ggplot(df2, aes(x=nboot, y=boot)) +
  geom_boxplot(outlier.shape=NA) + #avoid plotting outliers twice
  geom_jitter(aes(color=nboot), position=position_jitter(width=.2, height=0)) +
  labs(title="", y = "", x = "nboot")

If we omit the outlier.shape=NA option in geom_boxplot(), we will get the following plot.

Jitterboxplot.png

Violin plot

library(ggplot2)
ggplot(midwest, aes(state, area)) + geom_violin() + ggforce::geom_sina()

Violinplot.png

Kernel density plot

Back to back barplot

ggedit & ggplotgui – interactive ggplot aesthetic and theme editor

esquisse (French, means 'sketch'): creating ggplot2 interactively

https://cran.rstudio.com/web/packages/esquisse/index.html

A 'shiny' gadget to create 'ggplot2' charts interactively with drag-and-drop to map your variables. You can quickly visualize your data accordingly to their type, export to 'PNG' or 'PowerPoint', and retrieve the code to reproduce the chart.

The interface introduces basic terms used in ggplot2:

  • x, y,
  • fill (useful for bars & boxplot & 2D density, not useful for scatterplot),
  • color,
  • size,
  • facet, split up your data by one or more variables and plot the subsets of data together.

plotly

R → plotly

ggconf: Simpler Appearance Modification of 'ggplot2'

https://github.com/caprice-j/ggconf

Plotting individual observations and group means

https://drsimonj.svbtle.com/plotting-individual-observations-and-group-means-with-ggplot2

subplot

Easy way to mix multiple graphs on the same page

x and y labels

https://stackoverflow.com/questions/10438752/adding-x-and-y-axis-labels-in-ggplot2 or the Labels part of the cheatsheet

You can set the labels with xlab() and ylab(), or make it part of the scale_*.* call. 

labs(x = "sample size", y = "ngenes (glmnet)")

Prevent sorting of x labels

See Change the order of a discrete x scale.

The idea is to set the levels of x variable. 

junk   # n x 2 table
colnames(junk) <- c("gset", "boot")
junk$gset <- factor(junk$gset, levels = as.character(junk$gset))
ggplot(data = junk, aes(x = gset, y = boot, group = 1)) + 
  geom_line() + 
  theme(axis.text.x=element_text(color = "black", angle=30, vjust=.8, hjust=0.8))

Legend title

scale_colour_manual("Treatment", values = c("black", "red"))

ylim and xlim in ggplot2

https://stackoverflow.com/questions/3606697/how-to-set-limits-for-axes-in-ggplot2-r-plots or the Zooming part of the cheatsheet

Use one of the following

  • + scale_x_continuous(limits = c(-5000, 5000))
  • + coord_cartesian(xlim = c(-5000, 5000))
  • + xlim(-5000, 5000)

Center title

See the Legends part of the cheatsheet. 

ggtitle("MY TITLE") +
  theme(plot.title = element_text(hjust = 0.5))

Time series plot

Multiple lines plot https://stackoverflow.com/questions/14860078/plot-multiple-lines-data-series-each-with-unique-color-in-r 

set.seed(45)
nc <- 9
df <- data.frame(x=rep(1:5, nc), val=sample(1:100, 5*nc), 
                   variable=rep(paste0("category", 1:nc), each=5))
# plot
# http://colorbrewer2.org/#type=qualitative&scheme=Paired&n=9
ggplot(data = df, aes(x=x, y=val)) + 
    geom_line(aes(colour=variable)) + 
    scale_colour_manual(values=c("#a6cee3", "#1f78b4", "#b2df8a", "#33a02c", "#fb9a99", "#e31a1c", "#fdbf6f", "#ff7f00", "#cab2d6"))

Versus old fashion 

dat <- matrix(runif(40,1,20),ncol=4) # make data
matplot(dat, type = c("b"),pch=1,col = 1:4) #plot
legend("topleft", legend = 1:4, col=1:4, pch=1) # optional legend

Github style calendar plot

geom_errorbar(): error bars

set.seed(301)
x <- rnorm(10)
SE <- rnorm(10)
y <- 1:10

par(mfrow=c(2,1))
par(mar=c(0,4,4,4))
xlim <- c(-4, 4)
plot(x[1:5], 1:5, xlim=xlim, ylim=c(0+.1,6-.1), yaxs="i", xaxt = "n", ylab = "", pch = 16, las=1)
mtext("group 1", 4, las = 1, adj = 0, line = 1) # las=text rotation, adj=alignment, line=spacing
par(mar=c(5,4,0,4))
plot(x[6:10], 6:10, xlim=xlim, ylim=c(5+.1,11-.1), yaxs="i", ylab ="", pch = 16, las=1, xlab="")
arrows(x[6:10]-SE[6:10], 6:10, x[6:10]+SE[6:10], 6:10, code=3, angle=90, length=0)
mtext("group 2", 4, las = 1, adj = 0, line = 1)

Stklnpt.svg

text labels on scatterplots: ggrepel package

ggrepel package. Found on Some datasets for teaching data science by Rafael Irizarry.

Fonts

Adding Custom Fonts to ggplot in R

Save the plots

ggsave()

graphics::smoothScatter

smoothScatter with ggplot2

BBC

Add your brand to ggplot graph

You Need to Start Branding Your Graphs. Here's How, with ggplot!

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