plotTranscripts: Scatterplot or MA plot
In robertdouglasmorrison/DuffyTools: Duffy Lab Utility Tools

plotTranscripts

R Documentation

Scatterplot or MA plot

Description

Scatter or MA plots of trancriptomes or differential expression (DE) files

Usage

plotTranscripts(file1, file2, fid1 = basename(file1), fid1 = basename(file1), 
		geneColumn = "GENE_ID", value1Column = "RPKM_M", 
		value2Column = value1Column, cex = 1, units1 = "RPKM", units2 = units1,
		offset = 1, keepIntergenics = FALSE, 
		label = "Plot", plotType = c("Scatter", "MA"), 
		marker.genes = NULL, marker.col = 1, marker.cex = 1, 
		marker.labels = TRUE, marker.pch = 1,
		minYmax = NULL, sep = "\t", sym.asp = TRUE, hideZero = FALSE,
		showAllGenes = FALSE)

plotRatios(file, geneColumn = "GENE_ID", value1Column = "RPKM_1_M", value2Column = "RPKM_2_M", 
		cex = 1, units = "RPKM", offset = 1, keepIntergenics = FALSE, 
		label = "Plot", plotType = c("Scatter", "MA"), 
		marker.genes = NULL, marker.col = 1, marker.cex = 1, 
		marker.labels = TRUE, marker.pch = 1,
		minYmax = NULL, sep = "\t", sym.asp = TRUE, lab1 = "", lab2 = "",
		hideZero = FALSE)

plotRatiosTwoFiles(file1, file2, fid1 = basename(file1), fid1 = basename(file1), 
		geneColumn = "GENE_ID", valueColumn = "LOG_2_FOLD_M", 
		cex = 1, units = "Log2 Fold", offset = 0, keepIntergenics = FALSE, 
		label = "Plot", marker.genes = NULL, marker.col = 1, marker.cex = 1, 
		marker.labels = TRUE, marker.pch = 1,
		minYmax = NULL, sep = "\t", sym.asp = TRUE, hideZero = FALSE)

Arguments

`file`, `file1`, `file2`	character string, full pathname to existing transcript or DE file
`fid1`, `lab1`	sampleID text label for file 1, added to X axis
`fid2`, `lab2`	sampleID text label for file 2, added to Y axis
`geneColumn`	name of the column that contains GeneIDs
`valueColumn`	name of the column(s) that contains expression (or DE) data
`cex`	expansion factor for plotted points
`units`	character string of expression units, added to plot labels
`offset`	linear offset added to expression data, to prevent divide by zero during log transform, etc.
`keepIntergenics`	logical, keep the explicit 'non-genes' or drop them from the plot
`label`	text for the main plot label
`plotType`	type of plot. Either scatterplot or the MA plot typical of microarrays
`marker.genes`	character vector of GeneIDs to be highlighted, or `"identify"` to select by mouse clicks.
`marker.col`	color for highlighted gene points
`marker.cex`	expansion factor for highlighted genes
`marker.labels`	logical, add the GeneIDs for the marker genes to the plot
`marker.pch`	'pch' parameter for the symbol for the marker genes
`minYmax`	explicit control for the Y axis upper, useful for making making identical scaling over multiple plots
`hideZero`	logical, should genes with no expression be omitted.

Details

Function to standardize plotting of transcriptomes and DE result files. Suitable for comparing RNA-seq and microarray results. The 'Transcript' form can combine any 2 files of expression data. The 'Ratios' form takes its 2 transcripts from different columns within one differential expression file. The 'RatiosTwoFiles' form take differential expression fold change values from two separate files.

Value

In addition to a plot, these function return a list of data (subject to change) that currently includes:

`x`, `y`	the coordinates of the plotted points
`id`	the GeneIDs of those points
`Pearson_R`	the correlation coefficient
`Spearman_Rho`	the correlation coefficient