do.allPlots: Generate fusion expression plots

In jefferys/FusionExpressionPlot: Plot Expression Profiles for Fused Genes

Description

Given the fusions to plot and the normalized expression data assoicated with those fusions, outputs one fusion expression plot (as a pdf) for each. If multiple fusions from the same sample involve the same genes, these will be marked on one shared plot. [TODO - check if different gene order meand same or different plot]. Separate fusion expression plots are generated whenever fusions are in different samples, or when either involved gene is different.

Usage

do.allPlots(fusions, normalizedCohortExpression)

Arguments

fusions

A data frame describing the fusions to plot. One plot will be generated for each unique sample x fusion gene pair in this data frame. See getMapSpliceCohortFusionData for the expected structure.

normalizedCohortExpression

A data frame describing the gene models and the normalized exon expression data. See loadCohortDefinition and normExpressionData for the expected structure. Only the subset of the cohort associated with the fusions being plotted is needed, i.e. the gene-exon models for the genes involved + the normalized expression data columns for those exons for the samples involved. However extra expression data is just ignored. It is perfectly fine to provide the whole cohort normalized exon expression data frame.

Value

The main output is the pdf files, but returns a list with two summary stat values:

plotCount	The number of plots generated.
fusionLineCount	The number of fusions in the input list to plot.

Note: these may not be the same number due to multiple fusions merged into one plot when they involve the same gene pair in the same sample.

jefferys/FusionExpressionPlot documentation built on May 19, 2019, 3:59 a.m.