GC_coordinates: Modify Coordinates in a GC Chart

In geneviewer: Gene Cluster Visualizations

Modify Coordinates in a GC Chart

Description

This function updates a GC chart by modifying the coordinates settings. It allows for showing or hiding tick values, applying custom tick values for the top and bottom axes, and supports several other customizations for specific or all clusters in the chart.

Usage

GC_coordinates(
  GC_chart,
  show = TRUE,
  tickValuesTop = NULL,
  tickValuesBottom = NULL,
  ticksFormat = NULL,
  tickStyle = list(),
  textStyle = list(),
  cluster = NULL,
  ...
)

Arguments

GC_chart	The GC chart object to be modified.
show	Logical, whether to show the tick values or not. Can be a single value or a vector.
tickValuesTop	Numeric vector or NULL, custom tick values to be used at the top of the cluster. If NULL, the default tick values are used.
tickValuesBottom	Numeric vector or NULL, custom tick values to be used at the bottom of the cluster. If NULL, the default tick values are used.
ticksFormat	Format for tick labels. Default is ",.0f".
tickStyle	List, styling options for the ticks.
textStyle	List, styling options for the text. the coordinate modifications. If NULL, applies to all clusters.
cluster	Numeric or character vector or NULL; specifies which clusters to generate coordinates for. If NULL, labels will be applied to all clusters. Default is NULL.
...	Additional arguments to be passed to the coordinate options.

Value

Returns the GC chart object with updated coordinates.

Examples

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

# Add coordinates to all clusters
GC_chart(genes_data, cluster = "cluster", group = "name", height = "200px") %>%
GC_coordinates()

# Modify coordinates of a specific cluster
GC_chart(genes_data, cluster = "cluster", group = "name", height = "200px") %>%
GC_coordinates() %>%
GC_coordinates(
  cluster = 2,
  show = TRUE,
  tickValuesTop = c(130, 170, 210, 240),
  tickValuesBottom = c(160, 200),
  ticksFormat = ",.0f", # ".2s",
  rotate = -45,
  yPositionTop = 55,
  yPositionBottom = 45,
  overlapThreshold = 20,
  tickStyle = list(
  stroke = "black",
  strokeWidth = 1,
  lineLength = 6
  ),
  textStyle = list(
  fill = "black",
  fontSize = "12px",
  fontFamily = "Arial",
  cursor = "default"
  )
)

geneviewer documentation built on April 12, 2025, 9:12 a.m.