Modify Coordinates in a GC Chart

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

r

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

Arguments

Argument	Description
`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.
`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.
`groupStyle`	Named list of styles by group, applied to the coordinates of all genes of that group (the `group` of `GC_chart()`, or the column given in `style_by`). `show = FALSE` leaves out their coordinates, styles in `tick` go to their ticks and the other styles to their text, e.g. `list(other = list(show = FALSE), tnsA = list(fill = "red"))`. Only for the coordinates computed from the genes, not for `tickValuesTop` or `tickValuesBottom`.
`style_by`	Column name or NULL; the column whose values `groupStyle` is matched against. Default is NULL: the `group` of `GC_chart()`. the coordinate modifications. If NULL, applies to all clusters.
`...`	Additional arguments to be passed to the coordinate options.

Value

Returns the GC chart object with updated coordinates.

Examples

r

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"
  )
)