xhmmScripts (version 1.1)

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

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)