geneviewer (version 0.1.10)

GC_transcript: Modify Transcript Characteristics within a Chart

Description

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(),
  labelOptions = list(),
  ...
)

Value

Returns the modified gene chart object.

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.

customColors

List or NULL, custom colors to apply to the genes.

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.

labelOptions

List, options for styling labels such as font size, color, and position.

...

Additional arguments to be passed to the gene options.

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")
    )
  )