Add Links to GC Chart — GC_links • geneviewer

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 = NULL,
  measure = "identity",
  show_links = TRUE,
  label = TRUE,
  label_position = "gene",
  normal_color = NULL,
  inverted_color = NULL,
  low_color = NULL,
  vmin = NULL,
  vmax = NULL,
  use_group_colors = FALSE,
  color_bar = NULL,
  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. Default is NULL: as set by the theme, otherwise TRUE.
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. When the genes also have labels from GC_labels(), the measure is shown below the gene name in the same label (or after it, when the label is rotated to avoid overlap).
label_position: Where the measure labels go: "gene" (default), with the label of the gene as described for label, or "link", in the middle of each link, white on dark links. A measure is only written where it fits within its link and clear of the others, so narrow links stay clean; zoomed in with GC_zoom(), links widen and more of them are written. With "link", links from data have labels too.
normal_color: Color for the links in their normal state. Default is NULL: the color of the theme, otherwise "#969696".
inverted_color: Color for inverted links. Default is NULL: the color of the theme, otherwise "#d62728".
low_color: Color that links fade to at a low measure: links run from nearly this color (10% of the link color, at vmin) to normal_color or inverted_color (at vmax). Default is NULL: the color of the theme, otherwise white.
vmin, vmax: Numeric; the measures of the lightest and the full link color, also the ends of the color bar. Measures outside are drawn in the color of the nearest end. Default is NULL: as set by the theme, otherwise 0 and 100. Set vmin to the lowest measure to spread the colors over the data, e.g. vmin = floor(min(alignment$identity)).
use_group_colors: Logical; if TRUE, color links by group.
color_bar: Logical; if TRUE, the color bar is displayed. Default is NULL: as set by the theme, otherwise TRUE.
colorBarOptions: List of options to customize the color bar appearance: position, where the bar goes: a corner of the plot area, "bottomright" (default), "bottomleft", "topright" or "topleft", or "legend" for an item of the legend (GC_legend()), lying down, in the font of the legend; without a legend it goes bottom right. legendSide puts it before the groups of the legend, "left" (default), or after them, "right". orientation, "vertical" (default) or "horizontal". labels, for a horizontal bar: "inline", one line with the title, the lowest measure, the bar and the highest, or "below", the title above the bar and ticks with their measures below it, as many as fit. Default is "inline"; in the legend it is always inline, as its rows are one line. The title of a horizontal bar is bold. With the labels below, the bar is about three lines tall, so in a corner it is more likely to cover genes. In the legend the bar is as tall as the legend markers, with a light grey outline when the theme leaves it without one. x and y move the bar in from its corner (default 0, and 24 pixels up from a bottom corner for a vertical bar); width and height set the size of the bar (default 10 by 60 pixels standing, 80 by 8 lying inline, 120 by 8 lying with the labels below); title = FALSE leaves out its title; labelOptions, titleOptions and barOptions style the labels, the title and the bar. The bar is drawn over the plot area, so in a corner it can cover genes or links: move it with x and y, or put it in the legend.
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.

Value

Modified GC_chart object with added 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))


# A horizontal color bar in the legend
GC_chart(genes_data, cluster = "cluster", group = "group",
         height = "220px") %>%
  GC_links(group = "group", measure = "identity", label = FALSE,
           colorBarOptions = list(position = "legend")) %>%
  GC_legend(position = "top")


# 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()