In freestatman/ideogRam: ideogRam R htmlwidget

library(ideogRam)
library(GenomicRanges)

Human

A human genome is depicted below. The grey and black bands in each chromosome represent heterochromatin. The pink region is the area around the centromere, and the blue represents variable regions.

ideogRam(organism = "human", chrHeight = 500)

Mouse

ideogRam(
    organism = "mouse",
    orientation = "horizontal",
    showBandLabels = TRUE,
    chrHeight = 300
)

Annotations, basic

The location of BRCA1 is depicted here in red.

brca1 <- GRanges('17', IRanges(43044294, 43125482), name = "BRCA1")
# This seems a bug, as it shows chromosomes 1, 7 and 17.
ideogRam(organism = "human") %>%
    set_option(chromosomes = '17', chrHeight = 600, orientation = "horizontal") %>%
    set_option(showAnnotTooltip = TRUE) %>%
    add_track(brca1)

Annotations, overlaid

Large-scale structural variations (SVs) can be depicted using colored overlays, as seen below.

ten_virtual_cnvs <- ideogRam:::sample_10_virtual_cnvs()
ten_virtual_cnvs
ideogRam(organism = "human") %>%
    set_option(chrHeight = 300, chrMargin = 2, annotationsLayout = "overlay",
               orientation = "horizontal") %>%
    add_track(ten_virtual_cnvs)

Annotations, tracks

Layout, small

ideogRam(organism = "human", orientation = "vertical", rows = 2) %>%
    set_option(resolution = 550, chrHeight = 150, rotatable = FALSE)

Brush

ideogRam(
    organism = "human",
    chromosome = "1",
    resolution = 550,
    chrHeight = 600,
    orientation = "horizontal",
    brush = TRUE  ## In the new version, we need to give a string
)

Ploidy, basic

ideogRam(
    organism = "human",
    sex = "female",
    chrHeight = 300,
    chrWidth = 8,
    ploidy = 2
)

freestatman/ideogRam documentation built on Nov. 4, 2022, 1:55 p.m.