Modify Gene Characteristics within a Chart

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(),
  groupStyle = NULL,
  style_by = NULL,
  corner_radius = NULL,
  ...
)

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: a d3 scheme (e.g. "schemeSet2") or a geneviewer palette (e.g. "okabeIto", see geneviewer_palette()). When no cluster is selected, the legend uses the same colours. NULL keeps the colours set by GC_color().
customColors: List or NULL, custom colors to apply to the genes: a vector of colours, recycled over the groups, or a named list of colours by group. Groups left out of a named list keep the colours of the colour scheme. When no cluster is selected, the legend uses the same colours.
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.
groupStyle: Named list of styles by group, applied to every gene of that group (of group, or of the column given in style_by), e.g. list(promoter = list(marker = "box", fill = "grey")). Takes the same options as itemStyle; the itemStyle of a gene takes precedence over the style of its group.
style_by: Column name or NULL; the column whose values groupStyle is matched against, to style genes by another column than the one that sets their colours, or "geneTrack" for the track of a gene with GC_cluster()(prevent_gene_overlap = ), e.g. groupStyle = list("2" = list(markerHeight = 8)) to draw the genes of the second track smaller. Default is NULL: group.
corner_radius: Numeric or NULL, radius in pixels of the rounded corners of 'arrow', 'boxarrow', 'box' and 'rbox' markers, e.g. 3 for soft corners. The inner corners of arrows stay sharp. Default is NULL: sharp corners, and 5 for 'rbox'.
...: Additional arguments to be passed to the gene options.

Value

Returns the modified gene chart object.

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")
  )
 )


# Change the appearance of all genes of a group
GC_chart(genes_data, cluster = "cluster", group = "group", height = "200px") %>%
  GC_genes(groupStyle = list(C = list(marker = "box", stroke = "red")))