Package 'ggfun'

%<+%

Description

This operator attaches annotation data to a ggtree or ggsc graphic object

Usage

p %<+% data

Arguments

p	ggplot2 object, such as ggtree or ggsc graphic object.
data	data.frame, which must contains a column of node, or the first column of taxa labels, when p is a ggtree object. Or it must contains columns of .BarcodeID, when p is a ggsc object and p$data does not contain a column of features, if it contains, the data must also contains a column of features.

Value

ggplot object with annotation data added

---

this element is used to control the line color of panel.grid.major/minor.x or panel.grid.major/minor.y

Description

this element is used to control the line color of panel.grid.major/minor.x or panel.grid.major/minor.y

Usage

element_blinds(
  colour = c("white", "grey60"),
  axis,
  color = NULL,
  inherit.blank = FALSE
)

Arguments

colour	the colour of rectangular, default is c('white', 'grey60').
axis	character, require, option is y or x.
color	Color is an alias for colour
inherit.blank	Should this element inherit the existence of an element_blank among its parents? If TRUE the existence of a blank element among its parents will cause this element to be blank as well. If FALSE any blank parent element will be ignored when calculating final element state.

Examples

library(ggplot2)
df <- data.frame(
         x = rep(c(2, 5, 7, 9, 12), 2),
         y = rep(c(1, 2), each = 5),
         z = factor(rep(1:5, each = 2)),
         w = rep(diff(c(0, 4, 6, 8, 10, 14)), 2)
       )
ggplot(df, aes(x, y)) + geom_tile(aes(fill = z), colour = 'grey50') + 
theme(panel.grid.major.y = element_blinds(color= c('white', 'grey'), axis='y'))

---

round rectangle borders and backgrounds

Description

round rectangle borders and backgrounds

Usage

element_roundrect(
  fill = NULL,
  colour = NULL,
  size = NULL,
  linetype = NULL,
  color = NULL,
  r = grid::unit(0.1, "snpc"),
  inherit.blank = FALSE
)

Arguments

fill	Fill colour.
colour, color	Line/border colour. Color is an alias for colour.
size	text size in pts.
linetype	Line type. An integer (0:8), a name (blank, solid, dashed, dotted, dotdash, longdash, twodash), or a string with an even number (up to eight) of hexadecimal digits which give the lengths in consecutive positions in the string.
r	the radius of the rounded corners, a unit object, default is unit(0.1, 'snpc').
inherit.blank	Should this element inherit the existence of an element_blank among its parents? If TRUE the existence of a blank element among its parents will cause this element to be blank as well. If FALSE any blank parent element will be ignored when calculating final element state.

Examples

library(ggplot2)
p <- ggplot(mpg, aes(displ, cty)) + geom_point()
p <- p + facet_grid(cols = vars(cyl))
p <- p + theme(strip.background=element_roundrect(fill="grey40", color=NA, r=0.15))
p
p2 <- ggplot(mtcars, aes(mpg, disp, color=factor(cyl), size=cyl)) + 
      geom_point()
p2 + theme(legend.background=element_roundrect(color="#808080", linetype=2))

---

facet_set

Description

add a facet label to a ggplot or change facet label of a ggplot

Usage

facet_set(label, side = "t", angle = NULL)

Arguments

label	a character or a named vector to label the plot
side	to label the plot at which side, either 't' (top) or 'r' (right)
angle	angle of the facet label. Default is 0 for side='t' and -90 for side='r'.

Value

a ggplot with facet label

---

geom_cake

Description

ggplot2 layer of birthday cake

Usage

geom_cake(mapping = NULL, data = NULL, ...)

Arguments

mapping	aes mapping
data	data
...	additional parameters

Value

ggplot2 layer

Author(s)

Guangchuang Yu

Examples

library(ggplot2)
ggplot(mtcars, aes(mpg, disp)) + geom_cake()
library(ggplot2)
ggplot(mtcars, aes(mpg, disp)) + geom_cake()

---

geom_scatter_rect

Description

draw rectangle boxes as scatter points

Usage

geom_scatter_rect(
  mapping = NULL,
  data = NULL,
  asp = 0.6,
  width = 0.8,
  height = NULL,
  ...
)

Arguments

mapping	aesthetic mapping, default is NULL
data	input data, default is NULL
asp	aspect ration of rectangle box (height vs width), only works for height is missing
width	width of the rectangles, default is 0.8
height	height of the rectangles
...	additional parameters passed to 'geom_rect'

Author(s)

Guangchuang Yu

---

geom_segment_c

Description

geom_segment_c supports coloring segment with continuous colors

Usage

geom_segment_c(
  mapping = NULL,
  data = NULL,
  position = "identity",
  lineend = "butt",
  na.rm = FALSE,
  show.legend = NA,
  inherit.aes = TRUE,
  arrow = NULL,
  arrow.fill = NULL,
  ...
)

Arguments

mapping	aes mapping
data	data
position	position
lineend	lineend
na.rm	logical
show.legend	logical
inherit.aes	logical
arrow	specification for arrow heads, as created by arrow().
arrow.fill	fill color to usse for the arrow head (if closed). NULL means use colour aesthetic.
...	additional parameter

Value

add segment layer

Author(s)

Guangchuang Yu

See Also

geom_segment

Examples

set.seed(2019-06-28)
d = data.frame(x = rnorm(10),
              xend = rnorm(10),
              y = rnorm(10),
              yend = rnorm(10),
              v1 = rnorm(10),
              v2 = rnorm(10))
library(ggplot2)
ggplot(d) + geom_segment_c(aes(x = x, xend = xend, y=y, yend =yend, col0 = v1, col1 = v2)) +
   scale_color_viridis_c(name = "continuous colored lines") + 
   theme_minimal() + theme(legend.position=c(.2, .85)) + xlab(NULL) + ylab(NULL)

---

geom_triangle

Description

ggplot2 layer of triangle

Usage

geom_triangle(mapping = NULL, data = NULL, ...)

Arguments

mapping	aes mapping
data	data
...	additional parameters

Value

ggplot2 layer

Author(s)

Shipeng Guo

Examples

library(ggplot2)
ggplot(mtcars, aes(mpg, disp)) + geom_triangle()

---

geom_volpoint

Description

layer of scatter points for volcano plot to visualize differential genes

Usage

geom_volpoint(
  mapping = NULL,
  data = NULL,
  log2FC_cutoff = 2,
  p_cutoff = 1e-05,
  ...
)

Arguments

mapping	aesthetic mapping
data	input data set
log2FC_cutoff	cutoff values for log2FC
p_cutoff	cutoff values p-value or adjusted p-value
...	additional paramters passed to the layer

Value

a ggplot

---

get_aes_var

Description

extract aes mapping, compatible with ggplot2 < 2.3.0 & > 2.3.0

Usage

get_aes_var(mapping, var)

Arguments

mapping	aes mapping
var	variable

Value

mapped var

Author(s)

Guangchuang Yu

---

get_legend

Description

extract legend from a plot

Usage

get_legend(plot)

Arguments

plot	a gg or gtable object

Value

a 'gtable' object of the legend

Author(s)

Guangchuang Yu

---

get_plot_data

Description

extract data from a 'gg' plot

Usage

get_plot_data(plot, var = NULL, layer = NULL)

Arguments

plot	a 'gg' plot object
var	variables to be extracted
layer	specific layer to extract the data

Value

a data frame of selected variables

Author(s)

Guangchuang Yu

---

ggbreak2ggplot

Description

convert a ggbreak object to a ggplot object

Usage

ggbreak2ggplot(plot)

Arguments

plot	a ggbreak object

Value

a ggplot object

Author(s)

Guangchuang Yu

---

gglegend

Description

add manual setting legend

Usage

gglegend(mapping, data, geom, p = NULL)

Arguments

mapping	aes mapping for the 'geom'. The first mapping should be the one for the legend, while others maybe needed for the 'geom' (e.g., label for geom_text).
data	input data frame. If users want to mapping 'VALUE' to 'colour', the input data should contains 'VALUE' and 'colour' (actual value, e.g., 'red' and 'blue') variable.
geom	a geom to plot the data for generating the legend and the geom will be plotted invisible.
p	a ggplot object. If NULL, the 'last_plot()' will be used.

Details

add additional legend to a ggplot

Value

a ggplot object

Author(s)

Guangchuang Yu

Examples

library(ggplot2)
p <- ggplot(mtcars, aes(mpg, disp)) + geom_point()
data <- data.frame(colour = c("red",  "blue"), VALUE = c("A", "B"))
gglegend(aes(colour = VALUE, label=VALUE), data, geom_text, p)

---

identify

Description

identify node by interactive click

Usage

## S3 method for class 'gg'
identify(x = last_plot(), col = "auto", ...)

Arguments

x	tree view
col	selected columns to extract. Default is "auto" which will select all columns for 'ggplot' object and 'node' column for 'ggtree' object
...	additional parameters, normally ignored

Value

closest data point

Author(s)

Guangchuang Yu

---

is.ggbreak

Description

check whether a plot is a ggbreak object (including 'ggbreak', 'ggwrap' and 'ggcut' that defined in the 'ggbreak' package)

Usage

is.ggbreak(plot)

Arguments

plot	a plot obejct

Value

logical value

Author(s)

Guangchuang Yu

---

is.ggtree

Description

test whether input object is produced by ggtree function

Usage

is.ggtree(x)

Arguments

x

object

Value

TRUE or FALSE

Author(s)

Guangchuang Yu

---

keybox

Description

draw border for each of the ggplot legends

Usage

keybox(p, grob = "roundrect", gp = NULL)

Arguments

p	a ggplot object
grob	one of 'rect' or 'roundrect'
gp	graphic parameter

Value

grob object

Author(s)

Guangchuang Yu

Examples

library(ggplot2)
p <- ggplot(mtcars, aes(mpg, disp, color=factor(cyl), size=cyl)) + geom_point()
keybox(p, 'roundrect', gp = gpar(col = '#808080', lty = "dashed"))

---

set_font

Description

setting font for ggplot (axis text, label, title, etc.)

Usage

set_font(p, family = "sans", fontface = NULL, size = NULL, color = NULL)

Arguments

p	ggplot object
family	font fammily
fontface	font face
size	font size
color	font color

Value

TableGrob object

Author(s)

Guangchuang Yu

Examples

library(grid)
library(ggplot2)
d <- data.frame(x=rnorm(10), y=rnorm(10), lab=LETTERS[1:10])
p <- ggplot(d, aes(x, y)) + geom_text(aes(label=lab), size=5)
set_font(p, family="Times", fontface="italic", color='firebrick')

---

set_point_legend_shape

Description

override point legend set by 'aes(shape = I(shape))'

Usage

set_point_legend_shape(plot)

Arguments

plot	a 'gg' plot object

Value

an updated plot

Author(s)

Guangchuang Yu

---

td-filter

Description

filter data for tree annotation layer

Usage

td_filter(..., .f = NULL)

Arguments

...	Expressions that return a logical value.
.f	a function (if any, defaults to NULL) that pre-operate the data

Details

The 'td_filter()' function returns another function that can be used to subset ggtree() plot data. The function can be passed to the 'data' parameter of geom layer to perform subsetting. All rows that satisy your conditions will be retained.

Value

A function to filter ggtree plot data using conditions defined by '...'.

Author(s)

Guangchuang Yu

References

For more detailed demonstration of this function, please refer to chapter 12.5.1 of Data Integration, Manipulation and Visualization of Phylogenetic Trees http://yulab-smu.top/treedata-book/index.html by Guangchuang Yu.

See Also

filter

Examples

## Not run: 
tree <- rtree(30)
## similar to 'ggtree(tree) + geom_tippoint()'
ggtree(tree) + geom_point(data = td_filter(isTip))

## End(Not run)

---

td-mutate

Description

mutate data for tree annotation layer

Usage

td_mutate(..., .f = NULL)

Arguments

...	additional parameters that pass to dplyr::mutate
.f	a function (if any, defaults to NULL) that pre-operate the data

Details

The 'td_mutate()' function returns another function that can be used to mutate ggtree() plot data. The function can be passed to the 'data' parameter of geom layer to perform adding new variables and preserving existing ones.

Value

A function to mutate ggtree plot data

See Also

mutate

---

td-unnest

Description

flatterns a list-column of data frame

Usage

td_unnest(cols, ..., .f = NULL)

Arguments

cols	columns to unnest
...	additional parameters that pass to tidyr::unnest
.f	a function (if any, defaults to NULL) that pre-operate the data

Details

The 'td_unnest' function returns another function that can be used to unnest ggtree() plot data. The function can be passed to the 'data' parameter of a geom layer to flattern list-cloumn tree data.

Value

A function to unnest ggtree plot data

Author(s)

Guangchuang Yu

References

For demonstration of this function, please refer to chapter 12.5.2 of Data Integration, Manipulation and Visualization of Phylogenetic Trees http://yulab-smu.top/treedata-book/index.html by Guangchuang Yu.

See Also

unnest

---

the theme of blind-like

Description

the theme of blind-like

Usage

theme_blinds(colour = c("white", "grey"), axis = "y", ...)

Arguments

colour	the colour of rectangular, default is c('white', 'grey60').
axis	character which grid of axis will be filled, default is 'y'.
...	additional parameters that passed to theme function.

Value

ggplot2 theme

Examples

library(ggplot2)
iris |> tidyr::pivot_longer(
    cols = !Species,
    names_to = 'var',
    values_to = 'value'
  ) |>
ggplot(
  aes(x=var, y=Species, color=value, size=value)
) +
geom_point() -> p
p +
theme_blinds(
  colour = c('grey90', 'white'),
  axis = 'y',
  axis.line.y=element_line()
)
p +
theme_blinds(
  colour = c('grey90', 'white'),
  axis = 'x',
  axis.line.x = element_line()
)

---

theme_fp

Description

theme format painter

Usage

theme_fp(x, i)

Arguments

x	ggplot object to provide theme format
i	the element of a theme provided by x

Details

It applies theme element (i) from a ggplot (x) to another ggplot object

Value

theme element

Author(s)

Guangchuang Yu and Shuangbin Xu

---

theme_no_margin

Description

A theme that has no margin

Usage

theme_no_margin(...)

Arguments

...	additional parameters that passed to theme()

Value

ggplot2 theme

Author(s)

Guangchuang Yu

---

theme_nothing

Description

A theme that only show the plot panel

Usage

theme_nothing(base_size = 11, base_family = "")

Arguments

base_size	font size
base_family	font family

Value

ggplot2 theme

Author(s)

Guangchuang Yu

---

theme_noxaxis

Description

A theme that only show y-axis

Usage

theme_noxaxis(color = "black", ...)

theme_noyaxis(color = "black", ...)

theme_noaxis(...)

Arguments

color	color of y-axis
...	additional parameters that passed to theme()

Value

ggplot2 theme

Author(s)

Guangchuang Yu

---

the theme of blind-like alias of theme_blinds

Description

the theme of blind-like alias of theme_blinds

Usage

theme_stamp(colour = c("white", "grey"), axis = "y", ...)

Arguments

colour	the colour of rectangular, default is c('white', 'grey60').
axis	character which grid of axis will be filled, default is 'y'.
...	additional parameters that passed to theme function.

---

theme_transparent

Description

transparent background theme

Usage

theme_transparent(...)

Arguments

...	additional parameter to tweak the theme

Value

ggplot object

Author(s)

Guangchuang Yu with contributions from Hugo Gruson

---

volplot

Description

volcano plot

Usage

volplot(data, mapping, log2FC_cutoff = 2, p_cutoff = 1e-05, ...)

Arguments

data	input data set
mapping	aesthetic mapping
log2FC_cutoff	cutoff values for log2FC
p_cutoff	cutoff values p-value or adjusted p-value
...	additional paramters passed to the 'geom_volpoint' layer

Value

a ggplot

---

plot range of a ggplot object

Description

extract x or y ranges of a ggplot

Usage

yrange(gg, type = "limit", region = "panel")

xrange(gg, type = "limit", region = "panel")

ggrange(gg, var, type = "limit", region = "panel")

Arguments

gg	a ggplot object
type	one of 'limit' or 'range', if 'region == "plot"', to extract plot limit or plot data range
region	one of 'panel' or 'plot' to indicate extracting range based on the plot panel (scale expand will be counted) or plot data (scale expand will not be counted)
var	either 'x' or 'y'

Value

range of selected axis

Author(s)

Guangchuang Yu

---