Update Scale of a GC Chart Cluster

Modify the scale settings for specified clusters within a GC chart.

Usage

r

GC_scale(
  GC_chart,
  cluster = NULL,
  start = NULL,
  end = NULL,
  padding = NULL,
  hidden = FALSE,
  breaks = list(),
  tickValues = NULL,
  reverse = FALSE,
  axis_position = NULL,
  axis_type = "position",
  y = NULL,
  scale_breaks = FALSE,
  scale_break_threshold = 20,
  scale_break_padding = 1,
  ticksCount = NULL,
  ticksFormat = NULL,
  tickStyle = list(),
  textStyle = list(),
  lineStyle = list(),
  ...
)

Arguments

Argument	Description
`GC_chart`	A GC chart object.
`cluster`	Numeric or character vector specifying clusters in the GC chart to update.
`start`	Numeric vector indicating the starting point for the scale. Default is NULL.
`end`	Numeric vector indicating the end point for the scale. Default is NULL.
`padding`	Numeric value or percentage string indicating the padding on either side of the scale. The value can be a number or a string in the format of '2%'. Default is NULL: as set by the theme, otherwise 2.
`hidden`	Logical flag indicating whether the axis is hidden. Default is FALSE.
`breaks`	The scale breaks: stretches of the scale that are left out, with break marks on the line. Either a list of breaks for all selected clusters, e.g. `list(list(start = 5486, end = 9336))`, or a data frame with `start` and `end` columns and, for breaks per cluster, a `cluster` column. Positions are those of the data, also with `axis_type = "range"`. Default is an empty list ().
`tickValues`	Numeric vector or NULL, custom tick values to be used at the top of the cluster. If NULL, the default tick values are used.
`reverse`	Logical flag indicating whether to reverse the scale for the corresponding cluster. Default is FALSE.
`axis_position`	Character string indicating the type of the axis ('top' or bottom'). Default is NULL: as set by the theme, otherwise 'bottom'.
`axis_type`	Character string indicating the type of the axis ('position' or 'range'). Default is 'position'.
`y`	Numeric value from 1 to 100 indicating the y-position of the x-axis. Default is NULL.
`scale_breaks`	Logical flag indicating if scale breaks should be employed. Default is FALSE.
`scale_break_threshold`	Numeric value indicating the threshold percentage for determining scale breaks. Default is 20.
`scale_break_padding`	The room left on either side of a scale break: a number, as a percentage of the region shown (without its breaks), or a string in base pairs, e.g. `"500bp"`, for the same room around every break. Default is 1.
`ticksCount`	Numeric value indicating the number of ticks on the scale. Default is NULL: as set by the theme, otherwise 10.
`ticksFormat`	Format for tick labels; depends on axis_type, defaulting to ",.0f" for 'position' or ".2s" for 'range' when NULL.
`tickStyle`	List specifying the style for the ticks.
`textStyle`	List specifying the style for the tick text.
`lineStyle`	List specifying the style for the axis line.
`...`	Additional arguments for scale settings.

Value

Updated GC chart with new scale settings.

Examples

r

genes_data <- data.frame(
  start = c(100, 1000, 2000),
  end = c(150, 1500, 2500),
  name = c('Gene 4', 'Gene 5', 'Gene 6'),
  group = c('B', 'A', 'C'),
  cluster = c(2, 2, 2)
)
#Example usage with all custom options
GC_chart(genes_data, cluster = "cluster", group = "group", height = "200px") %>%
  GC_scale(
    start = 1,
    end = 2600,
    padding = 2,
    hidden = FALSE,
    reverse = FALSE,
    axis_position = "bottom",
    # breaks = list(
    #  list(start = 160, end = 900),
    #  list(start = 1600, end = 1900)
    # ),
    # tickValues = c(1, 2600),
    scale_breaks = TRUE,
    scale_break_threshold = 20,
    scale_break_padding = 1,
    ticksCount = 10,
    ticksFormat = ",.0f",
    y = NULL,
    tickStyle =
      list(
        stroke = "grey",
        strokeWidth = 1,
        lineLength = 6
        # Any other CSS styles
      ),
    textStyle =
      list(
        fill = "black",
        fontSize = "10px",
        fontFamily = "Arial",
        cursor = "default"
        # Any other CSS styles
      ),
    lineStyle = list(
      stroke = "grey",
      strokeWidth = 1
      # Any other CSS styles
    )
  ) %>%
  GC_legend(FALSE)