Generate a ChIP signal heatmap for a given sample.
#' @description This function plots the ChIP signal heatmap for the given set of target region. ChIP signals shown in the plot will be plotted as an output of EnrichedHeatmap::normalizeToMatrix().
Source: R/chip_related.R
get_chip_signal_heatmap.RdGenerate a ChIP signal heatmap for a given sample.
#' @description This function plots the ChIP signal heatmap for the given set of target region. ChIP signals shown in the plot will be plotted as an output of EnrichedHeatmap::normalizeToMatrix().
Usage
get_chip_signal_heatmap(
path_to_bw_file,
target_region,
extend = 5000,
background = NA,
mean_mode = "w0",
w = 50,
smooth = TRUE,
target_ratio = 0,
name = NULL,
col = NULL,
column_title = NULL,
axis_name = NULL,
top_annotation = NULL,
...
)Arguments
- path_to_bw_file
a character string denoting a path to a bw file. String can be an absolute path or the valid URL pointing to bw file.
- target_region
an object of the class GenomicRanges. Singal will be plotted against this regions.
- extend
pass to the same argument of
EnrichedHeatmap::normalizeToMatrix().- background
pass to the same argument of
EnrichedHeatmap::normalizeToMatrix().- mean_mode
pass to the same argument of
EnrichedHeatmap::normalizeToMatrix().- w
pass to the same argument of
EnrichedHeatmap::normalizeToMatrix().- smooth
pass to the same argument of
EnrichedHeatmap::normalizeToMatrix().- target_ratio
pass to the same argument of
EnrichedHeatmap::normalizeToMatrix().- name
pass to the same argument of
EnrichedHeatmap::EnrichedHeatmap().- col
pass to the same argument of
EnrichedHeatmap::EnrichedHeatmap().- column_title
pass to the same argument of
EnrichedHeatmap::EnrichedHeatmap().- axis_name
pass to the same argument of
EnrichedHeatmap::EnrichedHeatmap().- top_annotation
pass to the same argument of
EnrichedHeatmap::EnrichedHeatmap().- ...
Other arguments pass to
EnrichedHeatmap::EnrichedHeatmap().
Value
an output of the function EnrichedHeatmap::EnrichedHeatmap().