Package 'ggtangle'

category-item network plot

Description

category-item network plot

Usage

cnetplot(
  x,
  layout = igraph::layout_nicely,
  showCategory = 5,
  color_category = "#E5C494",
  size_category = 1,
  color_item = "#B3B3B3",
  size_item = 1,
  color_edge = "grey",
  size_edge = 0.5,
  categorySizeBy = ~itemNum,
  node_label = "all",
  foldChange = NULL,
  fc_threshold = NULL,
  hilight = "none",
  hilight_alpha = 0.3,
  ...
)

## S3 method for class 'list'
cnetplot(
  x,
  layout = "nicely",
  showCategory = 5,
  color_category = "#E5C494",
  size_category = 1,
  color_item = "#B3B3B3",
  size_item = 1,
  color_edge = "grey",
  size_edge = 0.5,
  categorySizeBy = ~itemNum,
  node_label = "all",
  foldChange = NULL,
  fc_threshold = NULL,
  hilight = "none",
  hilight_alpha = 0.3,
  ...
)

Arguments

x	input object
layout	network layout
showCategory	categories to display. Use a single number to show the first n categories, a numeric vector to select categories by index (for example, c(1, 10, 53)), or a character vector to select categories by name.
color_category	color of category node
size_category	relative size of the category
color_item	color of item node
size_item	relative size of the item (e.g., genes)
color_edge	color of edge, e.g., "black". If color = "category", then edges will be colored based on the category information.
size_edge	relative size of edge
categorySizeBy	An expression (e.g., itemNum, p.adjust) or a formula (e.g., ~ -log10(p.adjust)) to set the category node size.
node_label	one of 'all', 'none', 'category', 'item', 'exclusive' or 'share'
foldChange	numeric values to color the item (e.g, foldChange of gene expression values)
fc_threshold	threshold for absolute fold change to filter items
hilight	selected category to be highlighted
hilight_alpha	transparent value for not selected to be highlight
...	additional parameters. One important parameter is 'curvature' (default is 0), which can be used to curve the edges (e.g., curvature = 0.2).

Details

For list input, showCategory accepts either a single integer for the first n categories, a numeric vector of category indices, or a character vector of category names.

Examples

x <- list(A = letters[1:10], B = letters[5:12])
attr(x, "p.adjust") <- c(A = 0.01, B = 0.2)
p <- cnetplot(x, node_label = "none", categorySizeBy = ~ -log10(p.adjust))
p <- cnetplot(x, showCategory = c(1, 2))

---

Drag the nodes of a network to update the layout of the network

Description

Drag the nodes of a network to update the layout of the network

Usage

drag_network(p, g = NULL)

Arguments

p	the network diagram as a ggplot/gg/ggraph object.
g	an corresponding igraph object. Default is to extract from the 'ggraph' attribute.

Value

an updated ggplot/gg/ggraph object

Examples

## Not run: 
library(igraph)
library(ggraph)

flow_info <- data.frame(from = c(1,2,3,3,4,5,6),
                        to = c(5,5,5,6,7,6,7))
g = graph_from_data_frame(flow_info)
p <- ggraph(g, layout='nicely') + geom_node_point() + geom_edge_link() 
pp <- drag_network(p)

## End(Not run)

---

geom_cnet_label

Description

add labels of cnetplot

Usage

geom_cnet_label(mapping = NULL, data = NULL, node_label = "all", ...)

Arguments

mapping	aes mapping, default is NULL
data	plot data, default is NULL
node_label	which type of node label to be displayed, see also cnetplot
...	parameters that passed to geom_text_repel

Author(s)

Guangchuang Yu

---

layer to draw edges of a network

Description

layer to draw edges of a network

Usage

geom_edge(mapping = NULL, data = NULL, geom = geom_segment, ...)

Arguments

mapping	aesthetic mapping, default is NULL
data	data to plot, default is NULL
geom	geometric layer to draw lines
...	additional parameter passed to 'geom'

Value

line segments layer

Examples

flow_info <- data.frame(from = LETTERS[c(1,2,3,3,4,5,6)],
                        to = LETTERS[c(5,5,5,6,7,6,7)])

dd <- data.frame(
    label = LETTERS[1:7],
    v1 = abs(rnorm(7)),
    v2 = abs(rnorm(7)),
    v3 = abs(rnorm(7))
)

g = igraph::graph_from_data_frame(flow_info)

p <- ggplot(g)  + geom_edge()
library(ggplot2)
library(scatterpie)

p %<+% dd + 
    geom_scatterpie(cols = c("v1", "v2", "v3")) +
    geom_text(aes(label=label), nudge_y = .2) + 
    coord_fixed()

---

layer to draw edges of a network interactively

Description

layer to draw edges of a network interactively

Usage

geom_edge_interactive(
  mapping = NULL,
  data = NULL,
  geom = ggiraph::geom_segment_interactive,
  ...
)

Arguments

mapping	aesthetic mapping, default is NULL
data	data to plot, default is NULL
geom	geometric layer to draw lines
...	additional parameter passed to 'geom'

Value

line segments layer

Examples

library(ggiraph)
flow_info <- data.frame(from = LETTERS[c(1,2,3,3,4,5,6)],
                        to = LETTERS[c(5,5,5,6,7,6,7)])

dd <- data.frame(
    label = LETTERS[1:7],
    v1 = abs(rnorm(7)),
    v2 = abs(rnorm(7)),
    v3 = abs(rnorm(7))
)

g = igraph::graph_from_data_frame(flow_info)

p <- ggplot(g)  + geom_edge_interactive()
library(ggplot2)
library(scatterpie)

p2 <- p %<+% dd +
    geom_scatterpie(cols = c("v1", "v2", "v3")) +
    geom_text_interactive(aes(label=label, tooltip = label, data_id = label), nudge_y = .2) +
    coord_fixed()

girafe(ggobj = p2)

---

layer to draw edge labels of a network

Description

layer to draw edge labels of a network

Usage

geom_edge_text(
  mapping = NULL,
  data = NULL,
  geom = geom_text,
  angle_calc = "none",
  label_dodge = NULL,
  ...
)

Arguments

mapping	aesthetic mapping, default is NULL
data	data to plot, default is NULL
geom	geometric layer to draw text, default is geom_text
angle_calc	how to calculate angle ('along' or 'none')
label_dodge	dodge distance
...	additional parameter passed to 'geom'

Value

text layer

---

layer to draw edge labels of a network interactively

Description

layer to draw edge labels of a network interactively

Usage

geom_edge_text_interactive(
  mapping = NULL,
  data = NULL,
  geom = ggiraph::geom_text_interactive,
  angle_calc = "none",
  label_dodge = NULL,
  ...
)

Arguments

mapping	aesthetic mapping, default is NULL
data	data to plot, default is NULL
geom	geometric layer to draw text, default is geom_text
angle_calc	how to calculate angle ('along' or 'none')
label_dodge	dodge distance
...	additional parameter passed to 'geom'

Value

text layer

---

Circular layout

Description

Circular layout

Usage

layout_circular(graph, sort.by = NULL, ...)

Arguments

graph	A graph object.
sort.by	The attribute to sort the nodes by. Default is NULL.
...	Additional arguments passed to igraph::layout_in_circle.

Value

A matrix of coordinates.

Author(s)

Guangchuang Yu

---

Glycan Layout Algorithm (Fishbone/SNFG-like)

Description

Calculates node coordinates for a glycan structure to mimic SNFG style. Supports customizable direction and branch length.

Usage

layout_fishbone(graph, direction = "left", length = 1, angle_sep = 30, ...)

Arguments

graph	An igraph object.
direction	The direction of the main chain growth ("left", "right", "up", "down"). Default is "left".
length	The distance between nodes. Default is 1.
angle_sep	The angle separation for branches in degrees. Default is 30.
...	Additional arguments.

Value

A matrix of x, y coordinates.

---

Linear layout

Description

Linear layout

Usage

layout_linear(graph, sort.by = NULL, ...)

Arguments

graph	A graph object.
sort.by	The attribute to sort the nodes by. Default is NULL.
...	Additional arguments.

Value

A matrix of coordinates.

Author(s)

Guangchuang Yu

---