geneviewer (version 0.1.10)

GC_genes: Modify Gene Characteristics within a Chart

Description

This function updates a gene chart with specific characteristics for genes based on the given parameters. It can show/hide genes, apply a color scheme, assign custom colors, filter by cluster, and accept additional options.

Usage

GC_genes(
  GC_chart,
  group = NULL,
  marker = NULL,
  marker_size = NULL,
  show = TRUE,
  colorScheme = NULL,
  customColors = NULL,
  cluster = NULL,
  itemStyle = list(),
  ...
)

Value

Returns the modified gene chart object.

Arguments

GC_chart

The gene chart object to be modified.

group

Column name used for gene grouping to influence color aesthetics.

marker

Character or NULL, type of marker to represent genes on the chart. Allowed values are 'arrow', 'boxarrow', 'box', 'cbox', and 'rbox'.

marker_size

Character or NULL, size category of the marker ('small', 'medium', 'large').

show

Logical, whether to show the genes or not.

colorScheme

Character or NULL, the name of the color scheme to use.

customColors

List or NULL, custom colors to apply to the genes.

cluster

Numeric or character, the specific cluster to filter genes by.

itemStyle

List, a list of styles to apply to individual items in the chart.

...

Additional arguments to be passed to the gene options.

Examples

genes_data <- data.frame(
  start = c(10, 90, 130, 170, 210),
  end = c(40, 120, 160, 200, 240),
  name = c('Gene 1', 'Gene 3', 'Gene 4', 'Gene 5', 'Gene 6'),
  group = c('A', 'B', 'B', 'A', 'C'),
  cluster = c(1, 1, 2, 2, 2)
)

# Change the appearance of a specific gene cluster
GC_chart(genes_data, cluster = "cluster", group = "group", height = "200px") %>%
  GC_genes(
    group = "group",
    show = TRUE,
    marker = "arrow",
    marker_size = "medium",
    colorScheme = NULL, # One of D3.js build in colorSchemes
                        # (eg. "schemeCategory10",
                        # "schemeAccent", "schemeTableau10")
    customColors = NULL, # A vector of color names
    prevent_overlap = FALSE,
    gene_overlap_spacing = 40,
    cluster = 1, # Specify a specific cluster
    x = 1,
    y = 50,
    stroke = "black",
    strokeWidth = 1,
    arrowheadWidth = NULL,
    arrowheadHeight = NULL,
    arrowHeight = NULL,
    markerHeight = NULL # overwrites marker_size
   )

# Change the appearance of a specific gene
GC_chart(genes_data, cluster = "cluster", group = "group", height = "200px") %>%
GC_genes(
  cluster = 2,
  itemStyle = list(list(index = 2, fill = "red", stroke = "blue")
  )
 )