Add links generated by `get_links` to a `GC_chart` object. Links are added to the graph by their respective rowIDs.
Usage
GC_links(
GC_chart,
group = NULL,
data = NULL,
value1 = NULL,
value2 = NULL,
cluster = NULL,
curve = TRUE,
measure = "identity",
show_links = TRUE,
label = TRUE,
normal_color = "#969696",
inverted_color = "#d62728",
use_group_colors = FALSE,
color_bar = TRUE,
colorBarOptions = list(),
linkWidth = NULL,
linkStyle = list(),
labelStyle = list(),
...
)Arguments
- GC_chart
Gene chart object.
- group
The name of the column in the data to create value pairs from.
- data
data.frame containing linking data.
- value1
Optional vector of group values to generate links for.
- value2
Optional vector of group values to generate links for.
- cluster
Numeric or character vector or NULL; specifies which clusters.
- curve
Logical; if `TRUE`, links are curved, otherwise straight.
- measure
Character; specifies which measure to use for link color intensity. Should be "identity", "similarity", or "none".
- show_links
Logical; if `TRUE`, links are shown, otherwise hidden.
- label
Logical; if `TRUE`, shows measure labels on the links, otherwise hidden.
- normal_color
Color for the links in their normal state.
- inverted_color
Color for inverted links.
- use_group_colors
Logical; if `TRUE`, color links by group.
- color_bar
Logical; if `TRUE`, the color bar is displayed.
- colorBarOptions
List of options to customize the color bar appearance.
- linkWidth
Numeric; specifies the width of the links. A value of `1` represents full width, and `0` represents no width.
- linkStyle
A list of CSS styles to apply to the links.
- labelStyle
A list of CSS styles specifically for the labels.
- ...
Additional arguments passed to the links.
Examples
# Add links between all groups in each cluster
genes_data <- data.frame(
start = c(10, 90, 130, 170, 240, 250, 300, 340, 380, 420),
end = c(40, 120, 160, 200, 210, 270, 330, 370, 410, 450),
name = c('Gene 1', 'Gene 2', 'Gene 3', 'Gene 4', 'Gene 5',
'Gene 6', 'Gene 7', 'Gene 8', 'Gene 9', 'Gene 10'),
group = c('A', 'B', 'C', 'A', 'B', 'C', 'A', 'B', 'C', 'D'),
identity = c(NA, NA, NA, 50, 40, 100, 60, 65, 20, NA),
similarity = c(NA, NA, NA, 40, 30, 90, 50, 55, 10, NA),
cluster = c(1, 1, 1, 2, 2, 2, 3, 3, 3, 3)
)
GC_chart(genes_data,
cluster = "cluster",
height = "200px") %>%
GC_links(
group = "group",
value1 = "A",
value2 = "B",
measure = "identity",
label = FALSE) %>%
GC_labels(label = "group")
# Add links between group A of cluster 1 and A and B of cluster 2
GC_chart(genes_data,
cluster = "cluster",
height = "200px") %>%
GC_labels(label = "group") %>%
GC_links(group = "group",
value1 = c("A", "A"),
value2 = c("B", "A"),
label = FALSE,
cluster = c(1,2))
# Style links and color bar
GC_chart(genes_data,
cluster = "cluster",
height = "200px"
) %>%
GC_links(
group = "group",
data = NULL,
curve = TRUE,
measure = "identity",
show_links = TRUE,
label = TRUE,
normal_color = "#1f77b4",
inverted_color = "#d62728",
use_group_colors = FALSE,
color_bar = TRUE,
colorBarOptions = list(
x = 0,
y = 24,
width = 10,
height = 60,
labelOptions = list(
fontSize = 8,
xOffset = 2,
yOffset = 0
# Any other CSS style
),
titleOptions = list(
fontSize = 10,
xOffset = 2,
yOffset = 0
# Any other CSS style
),
barOptions = list(
stroke = "#000",
strokeWidth = 0.5,
opacity = 1
# Any other CSS style
)
),
linkWidth = 1,
linkStyle = list(
stroke = "black",
strokeWidth = 0.5,
fillOpacity = 0.4
# Any other CSS style
),
labelStyle = list(
fontSize = "8px"
# Any other CSS style
)
) %>%
GC_labels(label = "group", cluster = 1) %>%
GC_clusterLabel()