plotTranscripts: Scatterplot or MA plot

Description Usage Arguments Details Value

Description

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

Usage

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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


robertdouglasmorrison/DuffyTools documentation built on Dec. 14, 2018, 3:05 p.m.