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Fill Genes with Patterns

Source: R/chart_genes.R
GC_pattern.Rd

Fills the genes, exons and legend markers with a pattern per group, for example for black and white figures. Patterns can also be drawn on top of the gene colours to show each group with both a colour and a pattern.

Usage

GC_pattern(
  GC_chart,
  patterns = NULL,
  color = "black",
  background = "white",
  size = 6,
  strokeWidth = 1
)

Arguments

GC_chart

The gene chart object to be modified.

patterns

NULL, a vector of pattern names or a named list of pattern names by group. NULL gives each group a pattern in a fixed order. A vector is recycled over the groups. Available patterns: "none", "solid", "horizontal", "vertical", "diagonal", "antidiagonal", "grid", "crosshatch", "dots", "zigzag", "checkerboard", "rings", "bricks", "plus", "wideStripes" and "inverseDots" (background-coloured dots on a solid tile).

color

The colour of the pattern lines and dots: a single colour, a vector of colours recycled over the groups, or a named list of colours by group. For example, color = "white" with background = "black" gives white patterns on black.

background

The colour behind the pattern: a single colour, a vector of colours recycled over the groups, or a named list of colours by group. NULL keeps the gene colours set by GC_color(). When background is not NULL, intron lines and UTR outlines take color.

size

Numeric, the width and height of one pattern tile in pixels.

strokeWidth

Numeric, the width of the pattern lines in pixels.

Value

Returns the gene chart object with updated pattern settings.

Examples

genes_data <- data.frame(
  start = c(10, 50, 90, 130, 170, 210),
  end = c(40, 80, 120, 160, 200, 240),
  name = c('Gene 1', 'Gene 2', 'Gene 3', 'Gene 4', 'Gene 5', 'Gene 6'),
  group = c('A', 'A', 'B', 'B', 'A', 'C'),
  cluster = c(1, 1, 1, 2, 2, 2)
)

# Black and white
GC_chart(genes_data, cluster = "cluster", group = "group", height = "150px") %>%
  GC_pattern()



# Chosen patterns on grey backgrounds
GC_chart(genes_data, cluster = "cluster", group = "group", height = "150px") %>%
  GC_pattern(
    patterns = list(A = "dots", B = "crosshatch", C = "none"),
    background = c("white", "grey80")
  )



# Patterns on top of the gene colours
GC_chart(genes_data, cluster = "cluster", group = "group", height = "150px") %>%
  GC_pattern(background = NULL)



# White patterns on black for group C
GC_chart(genes_data, cluster = "cluster", group = "group", height = "150px") %>%
  GC_pattern(
    patterns = list(A = "checkerboard", B = "rings", C = "bricks"),
    color = list(A = "black", B = "black", C = "white"),
    background = list(A = "white", B = "white", C = "black")
  )