xhmmScripts (version 1.0)

plot_XHMM_region: Plot the XHMM CNV spanning the input region.

Description

Plot the XHMM CNV spanning the input region.

Usage

plot_XHMM_region(BASE_OUTPUT_NAME, xhmm_data, allTargsToGenes,
binarySampleFeatures, SQ_THRESH, chrom, start = NULL, stop = NULL,
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

chrom

start

stop

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

plot_XHMM_region("./out", xhmm_data, allTargsToGenes,
binarySampleFeatures, SQ_THRESH, "X", 10000, 20000)