Generate a ChIP signal heatmap of treatment over control.

This function plots the ChIP signal heatmap for the given set of target region. ChIP signals shown in the plot are the ratio of the treatment over control. Ratio will be calculated for each bin of the target region. Prior to calculate the ratio integer 1 will be added to both numerator and denominator to avoid the Inf and NaN from the final matrix.

Usage

get_chip_signal_over_control_heatmap(
  path_control_bw,
  path_treatment_bw,
  target_region = y,
  name_control = NULL,
  name_treatment = NULL,
  background = background,
  extend = extend,
  mean_mode = mean_mode,
  keep = c(0, 0.99),
  w = w,
  target_ratio = target_ratio,
  smooth = smooth,
  ...
)

Arguments

path_control_bw

a character string denoting a path to a bw file. String can be an absolute path or the valid URL pointing to bw file. Singals from this file will be used as numerator to calculate the fold change.

path_treatment_bw

a character string denoting a path to a bw file. String can be an absolute path or the valid URL pointing to bw file. Singals from this file will be used as denominator to calculate the fold change.

target_region

an object of the class GenomicRanges. Singal will be plotted against this regions.

name_control

a chanracter string denoting a name of the control sample. If NULL, the name will be derieved from the argument 'path_control_bw'.

name_treatment

a chanracter string denoting a name of the treatment sample. If NULL, the name will be derieved from the argument 'path_treatment_bw'.

background

pass to the same argument of EnrichedHeatmap::normalizeToMatrix().

extend

pass to the same argument of EnrichedHeatmap::normalizeToMatrix().

mean_mode

pass to the same argument of EnrichedHeatmap::normalizeToMatrix().

keep

pass to the same argument of EnrichedHeatmap::normalizeToMatrix().

w

pass to the same argument of EnrichedHeatmap::normalizeToMatrix().

target_ratio

pass to the same argument of EnrichedHeatmap::normalizeToMatrix().

smooth

pass to the same argument of EnrichedHeatmap::normalizeToMatrix().

...

other arguments pass to the function EnrichedHeatmap::EnrichedHeatmap().

Value

an object of the class Heatmap from the package ComplexHeatmap.

Details

To obtain the order of targets from the output heatmap the suggested approach is hm = ComplexHeatmap::draw(hm); ComplexHeatmap::row_order(hm).

Examples

if (FALSE) {

}