About ggplot2 for R

What is ggplot2

ggplot2 is a plotting system for R, based on the grammar of graphics, which tries to take the good parts of base and lattice graphics and none of the bad parts. It takes care of many of the fiddly details that make plotting a hassle (like drawing legends) as well as providing a powerful model of graphics that makes it easy to produce complex multi-layered graphics. – http://ggplot2.org/

Theme element functions

element_text()

Purpose: To control the drawing of labels and headings.

The table below lists the arguments of element_text() and their corresponding default values.

Argument	Description	Default value
family	font family	“”
face	font face	“plain”
colour	font color	“black”
size	font size (pts)	10
hjust	horizontal justification	0.5
vjust	vertical justification	0.5
angle	text angle	0
lineheight	line height	1.1

element_line()

Purpose: To draw lines and segments such as graphics region boundaries, axis tick marks and grid lines.

Argument	Description	Default value
colour	line color	“black”
size	line thickness	0.5
linetype	type of line	1

element_rect()

Purpose: To draw rectangles. It is mostly used for background elements and legend keys.

Argument	Description	Default value
fill	fill color	NA (none)
colour	border color	“black”
size	thickness of border line	0.5
linetype	type of border line	1 (solid)

element_blank()

Purpose: To draw nothing.

Arguments: none.

The element_blank() function can be applied to any theme element controlled by a theme element function.

With these functions in place, we now turn to the theme elements themselves.

Theme elements

Axis attributes

The table below lists each theme element associated with the rendering of axes, the theme function or unit function that controls it, and a short description of the element.

Element	Theme function	Unit	Description
axis.line	line		line parallel to axis
axis.text	text		tick labels
axis.text.x	text		x-axis tick labels
axis.text.y	text		y-axis tick labels
axis.title	text		axis titles
axis.title.x	text		x-axis title
axis.title.y	text		y-axis title
axis.ticks	line		axis tick marks
axis.ticks.length		cm	length of tick marks
axis.ticks.margin*		cm	width of axis tick margin

`axis.ticks.margin` is deprecated. Please set `margin` property of `axis.text` instead

Legend attributes

The following theme elements are associated with the appearance of legends:

Element	Theme function	Unit	Default value	Description
legend.background	rect			legend background
legend.key	rect			background of legend keys
legend.key.size		lines
legend.key.height		cm		legend key height
legend.key.width		cm		legend key width
legend.margin		lines		legend margin
legend.text	text			legend labels
legend.text.align			NULL	legend label alignment
legend.title	text			legend name
legend.title.align			NULL	legend name alignment
legend.position			“right”	position of legend
legend.direction	horizontal/vertical		NULL	direction of legend keys
legend.justification			“center”	justification of legend
legend.box	horizontal/vertical		NULL	position of multiple legend boxes

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p0 + theme(

legend.key = element_rect(fill = "yellow", color = "orange"),

legend.key.width = unit(0.5, "in"),

legend.key.height = unit(0.2, "in")

)

The following table summarizes the possible values for each legend theme element associated with positioning:

Theme element	Potential values
legend.direction, legend.box	“vertical”, “horizontal”
legend.position	“top”, “bottom”, “left”, “right” “none”
legend.justification	1st value: “left”, “center”, “right”
	2nd value: “top”, “center”, “bottom”

Panel attributes

Panel elements are associated with the graphics region in a ggplot. In faceted ggplots, these elements apply uniformly to each graphics panel.

Element	Theme function	Unit	Description
panel.background	rect		background of graphics region
panel.border	rect		border of graphics region
panel.grid.major	line		major grid lines
panel.grid.minor	line		minor grid lines
panel.margin		lines	margin between facets

Plot attributes

These elements pertain to the entire graphics region of a ggplot, but particularly outside a graphics panel (or the set of panels in a faceted plot).

Element	Theme function	Unit	Description
plot.background	rect		background of entire plot
plot.title	text		plot title
plot.margin		cm	vector of margins around plot

Sigmaplot Chart Standard

Title: Arial 14 Axis Title: Arial 12 Axis Text: Arial 10 Legend Text: Arial 10 All line thickness: 0.01in Major Tick Length: 0.05in Minor Tick Length: 0.03in

Dual axes

Follow instruction and code here. Notes: following packages needed:

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library(ggplot2)

library(gtable)

library(grid)

legend does not work, fix with here and the following code:

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## dual axis function

ggplot_dual_axis = function(plot1, plot2, which.axis = "x") {

# Update plot with transparent panel

plot2 = plot2 + theme(panel.background = element_rect(fill = NA))

grid.newpage()

# Increase right margin if which.axis == "y"

if(which.axis == "y") plot1 = plot1 + theme(plot.margin = unit(c(0.7, 1.5, 0.4, 0.4), "cm"))

# Extract gtable

g1 = ggplot_gtable(ggplot_build(plot1))

g2 = ggplot_gtable(ggplot_build(plot2))

# Overlap the panel of the second plot on that of the first

pp = c(subset(g1$layout, name == "panel", se = t:r))

g = gtable_add_grob(g1, g2$grobs[[which(g2$layout$name=="panel")]], pp$t, pp$l, pp$b, pp$l)

# Steal axis from second plot and modify

axis.lab = ifelse(which.axis == "x", "axis-b", "axis-l")

ia = which(g2$layout$name == axis.lab)

ga = g2$grobs[[ia]]

ax = ga$children[[2]]

# Switch position of ticks and labels

if(which.axis == "x") ax$heights = rev(ax$heights) else ax$widths = rev(ax$widths)

ax$grobs = rev(ax$grobs)

if(which.axis == "x")

ax$grobs[[2]]$y = ax$grobs[[2]]$y - unit(1, "npc") + unit(0.15, "cm") else

ax$grobs[[1]]$x = ax$grobs[[1]]$x - unit(1, "npc") + unit(0.15, "cm")

# Modify existing row to be tall enough for axis

if(which.axis == "x") g$heights[[2]] = g$heights[g2$layout[ia,]$t]

# Add new row or column for axis label

if(which.axis == "x") {

g = gtable_add_grob(g, ax, 2, 4, 2, 4)

g = gtable_add_rows(g, g2$heights[1], 1)

g = gtable_add_grob(g, g2$grob[[6]], 2, 4, 2, 4)

} else {

g = gtable_add_cols(g, g2$widths[g2$layout[ia, ]$l], length(g$widths) - 1)

g = gtable_add_grob(g, ax, pp$t, length(g$widths) - 1, pp$b)

g = gtable_add_grob(g, g2$grob[[7]], pp$t, length(g$widths), pp$b - 1)

}

# extract legend

leg1 <- g1$grobs[[which(g1$layout$name == "guide-box")]]

leg2 <- g2$grobs[[which(g2$layout$name == "guide-box")]]

legc = gtable:::cbind_gtable(leg1, leg2, "first")

g$grobs[[which(g$layout$name == "guide-box")]] <-

gtable:::cbind_gtable(leg1, leg2, "first")

grid.draw(g) # Note: Legend does not fit

#g$heights[[6]] = unit(5, "cm") # Add more space for the legend - can adjust this to suit

#grid.draw(g)

# Draw it

grid.draw(g)

}

Resources about themes

ggthemes for additional themes, a few publication theme for science, few, base and tufet details information about theme functions and elements here. A comprehensive tutorial is from here. yet another good site. inheritance tree can be ploted following here. default theme is theme_grey, theme_grey to list the full function code. theme_grey to list all the element.

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theme_grey()$axis.title.x

modify theme easily

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#based on a existing theme

theme_tan() <-theme_bw(base_size=16) +

theme(plot.title=element_text(margin = margin(5, 0, 15, 0),size=rel(1.2),face="bold"),

axis.title.x=element_text(margin = margin(10, 0, 0, 0),face="bold"),

axis.title.y=element_text(margin = margin(0, 10, 0, 0),face="bold"))

# or %+replace% to replace, anything did not touch in the children elements will be set to NULL

Random Notes

note-1

name	what is it	example code
lineheight	space between lines	g+theme(plot.title = element_text(size=20, face=”bold”, vjust=1, lineheight=0.6))
expression	expression	g<-g+labs(x=”Date”, y=expression(paste(“Temperature ( “, degree ~ F, ” )”)), title=”Temperature”)
vjust	Move the labels away from the plot (and add color)	g + theme(axis.title.x = element_text(color=”forestgreen”, vjust=-0.35),axis.title.y = element_text(color=”cadetblue” , vjust=0.35) )
ylim(), scale_x_continuous(), coord_cartesian()	ylim(), scale_x_continuous(), coord_cartesian()
name	change legend name	g+theme(legend.title = element_text(colour=”chocolate”, size=16, face=”bold”))+scale_color_discrete(name=”This color is\ncalled chocolate!?”)
legend.key	legend background box	g+theme(legend.key=element_rect(fill=’pink’))
guides(), guide_legend	size of legend symbols	g+guides(colour = guide_legend(override.aes = list(size=4)))

note-2

axis ticks face inwards in ggplot2.

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library(ggplot2)

library(grid)

ggplot(mtcars, aes(disp, mpg)) + geom_point() + theme_bw()+

theme(axis.ticks.length=unit(-0.25, "cm"),

# ***has to be set individually***

axis.text.x=element_text(margin=margin(20)),

axis.text.y=element_text(margin=margin(r=20))

)

ggolot.inward_tick.png

debug and margin for text (has to set individually for each axis as of version 2.1)

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library("ggplot2")

df <- data.frame(x = 1:3, y = 1:3)

plot <- ggplot(df, aes(x, y)) +

geom_point() +

ggtitle("An important plot")

plot

plot + theme(plot.title = element_text(margin = margin(b = 20)))

plot + theme(text = element_text(debug = TRUE))

ggolot.debug.png

border

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library("ggplot2")

ggplot(mtcars, aes(disp, mpg)) + geom_point() + theme_bw()+

theme(axis.ticks.length=unit(-0.25, "cm"))+

theme(axis.text.x = element_text(margin=margin(t=20)),

axis.text.y = element_text(margin=margin(r=20)),

axis.line.x=element_line(size=0.5),

panel.border=element_rect(size = 1,linetype = "solid",color = "red"))

Stat_Summary

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stat_sum_df <- function(fun, geom="crossbar", ...) {

stat_summary(fun.data=fun, colour="red", geom=geom, width=0.2, ...)

}

d + stat_sum_df("mean_cl_boot")

d + stat_sum_df("mean_cl_normal", geom = "errorbar")

Plot against index

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df %>%

gather(key, value, -id, -time) %>%

extract(key, c("question", "loop_number"), "(Q.\\..)\\.(.)") %>%

spread(question, value)

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