xhmmScripts (version 1.1)

plot_XHMM_genes: Plot the XHMM CNV spanning the input genes.

Description

Plot the XHMM CNV spanning the input genes.

Usage

plot_XHMM_genes(BASE_OUTPUT_NAME, xhmm_data, allTargsToGenes,
binarySampleFeatures, SQ_THRESH, genes,
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, EXACT_GENE_MATCH = FALSE, 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)

Arguments

BASE_OUTPUT_NAME

xhmm_data

allTargsToGenes

binarySampleFeatures

SQ_THRESH

genes

PLOT_ONLY_PNG

PLOT_LINE_SEGMENTS

DEFAULT_WIDTH

DEFAULT_HEIGHT

UPDATE_FIG_HEIGHT_FOR_MARGINS

GENE_NAME_cex

EXACT_GENE_MATCH

PLOT_PIPELINE_TRANSITIONS

DIFFERENTIATE_SAMPLE_GROUPS

COLOR_DIFFERENTIAL_TARGETS

MARK_SAMPLES

MARK_SAMPLES_COLORS

MARK_SAMPLES_ONLY_IN_CALLS

EXCLUDE_SAMPLES

MARK_INTERVALS

Examples

## Not run: plot_XHMM_genes("./out", xhmm_data,
# allTargsToGenes, binarySampleFeatures, SQ_THRESH, genes)## End(Not run)