Modify Transcript Characteristics within a Chart — GC

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

Usage

GC_transcript(
  GC_chart,
  transcript = NULL,
  type = NULL,
  strand = NULL,
  group = NULL,
  selection = NULL,
  show = TRUE,
  colorScheme = NULL,
  customColors = NULL,
  styleExons = list(),
  styleIntrons = list(),
  styleUTRs = list(),
  itemStyleExons = list(),
  itemStyleIntrons = list(),
  itemStyleUTRs = list(),
  groupStyleExons = NULL,
  groupStyleIntrons = NULL,
  groupStyleUTRs = NULL,
  style_by = NULL,
  labelOptions = list(),
  ...
)

Arguments

GC_chart: The chart object to be modified.
transcript: Optional column name used for clustering transcript data. Default is NULL.
type: Column name identifying the feature type ("UTR", "exon"). Default is NULL.
strand: Optional column name indicating strand orientation. Acceptable values include 1, 'forward', 'sense', or '+' to represent the forward strand, and -1, 0, 'reverse', 'antisense', "complement" or '-' to represent the reverse strand. Default is NULL, meaning strand information is not used.
group: Optional column name used for transcript grouping to influence color aesthetics.
selection: Numeric or character, the specific transcript to filter transcripts by.
show: Logical, whether to show the transcripts 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 selection is made, 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 selection is made, the legend uses the same colours.
styleExons: List, styles to apply to exons in the chart.
styleIntrons: List, styles to apply to introns in the chart.
styleUTRs: List, styles to apply to UTRs in the chart.
itemStyleExons: List, a list of styles to apply to individual exons in the chart.
itemStyleIntrons: List, a list of styles to apply to individual introns in the chart.
itemStyleUTRs: List, a list of styles to apply to individual UTRs in the chart.
groupStyleExons, groupStyleIntrons, groupStyleUTRs: Named lists of styles by group, applied to all exons, introns or UTRs of that group (of group, or of the column given in style_by), e.g. groupStyleExons = list(tx1 = list(fill = "red")). They take the same options as the matching itemStyle, which takes precedence.
style_by: Column name or NULL; the column whose values the group styles are matched against. Default is NULL: group.
labelOptions: List, options for styling labels such as font size, color, and position.
...: Additional arguments to be passed to the gene options.

Value

Returns the modified gene chart object.

Details

The first call of GC_transcript() makes the chart again with the transcripts as clusters. Settings of the whole chart made before it (e.g. GC_title(), GC_legend(), GC_theme() and the margins of GC_grid()) are kept. Settings per cluster (e.g. GC_labels(), GC_clusterTitle()) are for the old clusters: set them after GC_transcript().

Examples

transcript_data <- data.frame(
  transcript = c("transcript1", "transcript1", "transcript1", "transcript1",
                 "transcript2", "transcript2", "transcript2"),
  type = c("5_utr", "exon", "exon", "3_utr",
           "5_utr", "exon", "3_utr"),
  start = c(1, 101, 201, 301,
            1, 101, 301),
  end = c(50, 150, 250, 350,
          50, 150, 350),
  strand = rep("forward", 7)
)

# All default transcript settings
GC_chart(
  transcript_data,
  start = "start",
  end = "end",
  height = "200px"
) %>%
  GC_transcript(
    transcript = "transcript",
    strand = "strand",
    type = "type",
    group = NULL,
    show = TRUE,
    selection = NULL,
    colorScheme = NULL,
    customColors = NULL,
    styleExons = list(
      show = TRUE,
      strokeWidth = 0,
      cursor = "default",
      marker = "box",
      markerSize = "medium",
      arrowheadWidth = NULL,
      arrowheadHeight = NULL,
      markerHeight = NULL,
      cornerRadius = NULL
      # Any other CSS style
    ),
    styleIntrons = list(
      show = TRUE,
      strokeWidth = 1,
      fill = "none",
      cursor = "default",
      marker = "intron",
      markerSize = "medium",
      arrowheadWidth = NULL,
      arrowheadHeight = NULL,
      markerHeight = NULL,
      cornerRadius = NULL
      # Any other CSS style
    ),
    styleUTRs = list(
      show = TRUE,
      fontSize = "10px",
      fontStyle = "normal",
      fontFamily = "sans-serif",
      cursor = "default",
      color = "black",
      fill = "#FFF",
      strokeWidth = 1,
      marker = "box",
      markerSize = "medium",
      arrowheadWidth = NULL,
      arrowheadHeight = NULL,
      markerHeight = NULL,
      cornerRadius = NULL
      # Any other CSS style
    ),
    labelOptions = list(
      show = TRUE,
      xOffset = 2,
      yOffset = 0,
      fontSize = "12px",
      fontStyle = "normal",
      fontWeight = "normal",
      fontFamily = "sans-serif",
      cursor = "default",
      color = "black"
    ),
    itemStyleExons = list(),
    itemStyleIntrons = list(),
    itemStyleUTRs = list()
  )

# Change the appearance of a specific intron
GC_chart(transcript_data,
         start = "start",
         end = "end",
         height = "200px"
) %>%
  GC_transcript(
    transcript = "transcript",
    type = "type",
    selection = 2,
    itemStyleExons = list(list(index = 0, fill = "red")
    )
  )