plot_XHMM_targets: Plot the XHMM CNV spanning the input target indices.

In xhmmScripts: XHMM R scripts

Description

Plot the XHMM CNV spanning the input target indices.

Usage

plot_XHMM_targets(BASE_OUTPUT_NAME, xhmm_data, allTargsToGenes,
binarySampleFeatures, SQ_THRESH, startTarg, stopTarg,
PLOT_ONLY_PNG = TRUE, PLOT_LINE_SEGMENTS = TRUE, DEFAULT_WIDTH = 14,
DEFAULT_HEIGHT = 7, UPDATE_FIG_HEIGHT_FOR_MARGINS = TRUE, GENE_NAME_cex
= 0.8,
PLOT_PIPELINE_TRANSITIONS = TRUE, DIFFERENTIATE_SAMPLE_GROUPS = NULL,
COLOR_DIFFERENTIAL_TARGETS = TRUE, MARK_SAMPLES = NULL,
MARK_SAMPLES_COLORS = DEFAULT_MARK_SAMPLES_COLORS,
MARK_SAMPLES_ONLY_IN_CALLS = FALSE,
EXCLUDE_SAMPLES = NULL, MARK_INTERVALS = NULL, APPEND_REGION_NAME = TRUE)

Arguments

BASE_OUTPUT_NAME
xhmm_data
allTargsToGenes
binarySampleFeatures
SQ_THRESH
startTarg
stopTarg
PLOT_ONLY_PNG
PLOT_LINE_SEGMENTS
DEFAULT_WIDTH
DEFAULT_HEIGHT
UPDATE_FIG_HEIGHT_FOR_MARGINS
GENE_NAME_cex
PLOT_PIPELINE_TRANSITIONS
DIFFERENTIATE_SAMPLE_GROUPS
COLOR_DIFFERENTIAL_TARGETS
MARK_SAMPLES
MARK_SAMPLES_COLORS
MARK_SAMPLES_ONLY_IN_CALLS
EXCLUDE_SAMPLES
MARK_INTERVALS
APPEND_REGION_NAME

Examples

## Not run: plot_XHMM_targets("./out", xhmm_data, allTargsToGenes,
binarySampleFeatures, SQ_THRESH, 150, 180)
## End(Not run)

xhmmScripts documentation built on May 2, 2019, 1:01 a.m.