View source: R/view3dStructure.R
view3dStructure | R Documentation |
Plot xyz data with grid or rgl package.
view3dStructure(
p,
k = 3,
feature.gr,
atacSig,
lwd.backbone = 2,
col.backbone = "gray",
lwd.maxAtacSig = 8,
reverseATACSig = TRUE,
col.backbone_background = "gray70",
alpha.backbone_background = 0.5,
lwd.gene = 3,
coor_mark_interval = 5e+05,
col.coor = "black",
show_coor = TRUE,
coor_tick_unit = 50000,
label_gene = TRUE,
col.tension_line = "black",
lwd.tension_line = 1,
length.arrow = NULL,
safe_text_force = 3,
square = TRUE,
...
)
p |
GRanges object with mcols x, y, or with z |
k |
The dimension of plot. 2: 2d, 3: 3d. |
feature.gr |
The annotation features to be added. An object of GRanges. |
atacSig |
The ATAC-seq signals. An object of GRanges with scores or an object of track. |
lwd.backbone , lwd.gene , lwd.tension_line , lwd.maxAtacSig |
Line width for the linker, gene, interaction node circle, the dashed line of interaction edges, the tension line and the maximal reversed ATAC signal. |
col.backbone , col.backbone_background , col.tension_line , col.coor |
Color for the DNA chain, the compact DNA chain, the node circle, the linker, the tension line and the coordinates marker. |
reverseATACSig |
Plot the ATAC-seq signals in reverse values. |
alpha.backbone_background |
Alpha channel for transparency of backbone background. |
coor_mark_interval |
The coordinates marker interval. Numeric(1). Set to 0 to turn it off. The default value 1e5 means show coordinates every 0.1M bp. |
show_coor |
Plot ticks in the line to show the DNA compact tension. |
coor_tick_unit |
The bps for every ticks. Default is 1K. |
label_gene |
Show gene symbol or not. |
length.arrow |
Length of the edges of the arrow head (in inches). |
safe_text_force |
The loops to avoid the text overlapping. |
square |
A logical value that controls whether control points for the curve are created city-block fashion or obliquely. See grid.curve. |
... |
Not used. |
Coordinates for 2d.
p <- readRDS(system.file('extdata', '4DNFI1UEG1HD.chr21.FLAMINGO.res.rds',
package='trackViewer'))
feature.gr <- readRDS(system.file('extdata', '4DNFI1UEG1HD.feature.gr.rds',
package='trackViewer'))
view3dStructure(p, k=3, feature.gr=feature.gr, length.arrow=unit(0.000006, 'native'))
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