| circos.genomicTrackPlotRegion {circlize} | R Documentation |
Create a track for genomic graphics
Description
Create a track for genomic graphics
Usage
circos.genomicTrackPlotRegion(
data = NULL,
ylim = NULL,
stack = FALSE,
numeric.column = NULL,
jitter = 0,
panel.fun = function(region, value, ...) {NULL},
...)
Arguments
data |
A bed-file-like data frame or a list of data frames |
ylim |
If it is |
stack |
whether to plot in a "stack" mode. |
numeric.column |
Columns of numeric values in |
jitter |
Numeric. Only works for adding points in |
panel.fun |
Self-defined function which will be applied on each sector. Please not it is different
from that in |
... |
Pass to |
Details
Similar as circos.trackPlotRegion, users can add customized graphics by panel.fun, but the behaviour of panel.fun
will change depending on users' input data and stack setting.
When data is a single data frame, region in panel.fun is a data frame containing the second and third column in data in 'current' genomic category (e.g. current chromosome).
value is also a data frame containing columns in data excluding the first three columns.
When data is a list containing data frames, panel.fun will be applied iteratively on each data frame, thus,
region is extracted from the data frame which is in the current iteration. For example, if data contains two data frames, panel.fun
will be applied with the first data frame in current chromosome and then applied with the second data frame in the same chromosome.
If stack is set to TRUE, ylim will be re-defined. in stack mode, the y-axis will be splitted into several part
with equal height and graphics will be drawn on each 'horizontal' lines (y = 1, 2, ...). In this case:
When data is a single data frame containing one or more numeric columns, each numeric column defined in numeric.column will be treated as a single unit.
ylim is re-defined to c(0.5, n+0.5) in which n is number of numeric columns. panel.fun will be applied iteratively on each numeric column. In each
iteration, in panel.fun, region is still the genomic regions in current genomic category, but value contains current numeric column plus all non-numeric columns.
Under stack mode, in panel.fun, all low-level genomic graphical functions will draw on the 'horizontal line' y = i in which i is the index of current numeric column
and the value of i can be obtained by getI.
When data is a list containing data frames, each data frame will be treated as a single unit. The situation is quite similar as described in previous paragraph.
ylim is re-defined to c(0.5, n+0.5) in which n is number of data frames. panel.fun will be applied iteratively on each data frame. In each
iteration, in panel.fun, region is still the genomic regions in current genomic category, and value contains columns in current data frame excluding the first three columns.
Under stack mode, in panel.fun, all low-level genomic graphical functions will draw on the 'horizontal line' y = i in which i is the index of current data frame.
Being different from panel.fun in circos.trackPlotRegion, there should be an additional argument ... in panel.fun. This additional
argument is used to pass hidden values to low-level graphical functions. So if you are using functions like circos.genomicPoints, you should also
add ... as an additional argument into circos.genomicPoints.
See Also
https://jokergoo.github.io/circlize_book/book/genomic-plotting-region.html and https://jokergoo.github.io/circlize_book/book/modes-of-input.html
Examples
# There is no example
NULL