plotTranscripts | R Documentation |
Scatter or MA plots of trancriptomes or differential expression (DE) files
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)
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 |
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. |
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.
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 |
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