geneviewer (version 0.1.10)

GC_links: Add Links to GC Chart

Description

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(),
  ...
)

Value

Modified `GC_chart` object with added links.

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.

See Also

* [get_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()