circos.genomicHeatmap: Add heatmaps for selected regions

In jokergoo/circlize: Circular Visualization

Add heatmaps for selected regions

Description

Add heatmaps for selected regions

Usage

circos.genomicHeatmap(
    bed,
    col,
    na_col = "grey",
    numeric.column = NULL,
    border = NA,
    border_lwd = par("lwd"),
    border_lty = par("lty"),
    connection_height = mm_h(5),
    line_col = par("col"),
    line_lwd = par("lwd"),
    line_lty = par("lty"),
    heatmap_height = 0.15,
    side = c("inside", "outside"),
    track.margin = circos.par("track.margin"))

Arguments

bed	A data frame in bed format, the matrix should be stored from the fourth column.
col	Colors for the heatmaps. The value can be a matrix or a color mapping function generated by colorRamp2.
na_col	Color for NA values.
numeric.column	Column index for the numeric columns. The values can be integer index or character index. By default it takes all numeric columns from the fourth column.
border	Border of the heatmap grids.
border_lwd	Line width for borders of heatmap grids.
border_lty	Line style for borders of heatmap grids.
connection_height	Height of the connection lines. If it is set to NULL, no connection will be drawn. Use mm_h/cm_h/inches_h to set a height in absolute unit.
line_col	Color of the connection lines. The value can be a vector.
line_lwd	Line width of the connection lines.
line_lty	Line style of the connection lines.
heatmap_height	Height of the heatmap track
side	Side of the heatmaps. Is the heatmap facing inside or outside?
track.margin	Bottom and top margins.

Details

The function visualizes heatmaps which correspond to a subset of regions in the genome. The correspondance between heatmaps and regions are identified by connection lines.

The function actually creates two tracks, one track for the connection lines and one track for the heamtaps. The heatmaps always fill the whole track.

See Also

https://jokergoo.github.io/circlize_book/book/high-level-genomic-functions.html#genomic-heatmap

Examples

circos.initializeWithIdeogram(plotType = c("labels", "axis"))
bed = generateRandomBed(nr = 100, nc = 4)
col_fun = colorRamp2(c(-1, 0, 1), c("green", "black", "red"))
circos.genomicHeatmap(bed, col_fun, side = "inside", border = "white")
circos.genomicHeatmap(bed, col_fun, side = "outside", 
    line_col = as.numeric(factor(bed[[1]])))

jokergoo/circlize documentation built on Nov. 17, 2023, 11:32 a.m.