vsScatterPlot {vidger} | R Documentation |
This function allows you to visualize comparisons of log_{10} values of either FPKM or CPM measurements of two treatments depending on analytical type.
vsScatterPlot(x, y, data, d.factor = NULL, type = c("cuffdiff", "deseq", "edger"), title = TRUE, grid = TRUE, highlight = NULL, data.return = FALSE, xaxis.text.size = 10, yaxis.text.size = 10, xaxis.title.size = 12, yaxis.title.size = 12, main.title.size = 15)
x |
treatment |
y |
treatment |
data |
output generated from calling the main routines of either
|
d.factor |
a specified factor; for use with |
type |
an analysis classifier to tell the function how to process the
data. Must be either |
title |
display the main title of plot. Logical; defaults to
|
grid |
display major and minor axis lines. Logical; defaults to
|
highlight |
character string of IDs that will be highlighted. Set to
|
data.return |
returns data output of plot Logical; defaults to
|
xaxis.text.size |
change the font size of the |
yaxis.text.size |
change the font size of the |
xaxis.title.size |
change the font size of the |
yaxis.title.size |
change the font size of the |
main.title.size |
change the font size of the plot title text.
Defaults to |
An object created by ggplot
Brandon Monier, brandon.monier@sdstate.edu
# Cuffdiff example data("df.cuff") vsScatterPlot( x = "hESC", y = "iPS", data = df.cuff, d.factor = NULL, type = "cuffdiff", title = TRUE, grid = TRUE ) # DESeq2 example data("df.deseq") require(DESeq2) vsScatterPlot( x = "treated_paired.end", y = "untreated_paired.end", data = df.deseq, d.factor = "condition", type = "deseq", title = TRUE, grid = TRUE ) # edgeR example data("df.edger") require(edgeR) vsScatterPlot( x = "WW", y = "WM", data = df.edger, d.factor = NULL, type = "edger", title = TRUE, grid = TRUE ) # Highlight IDs data("df.cuff") hl <- c( "XLOC_000033", "XLOC_000099", "XLOC_001414", "XLOC_001409" ) vsScatterPlot( x = "hESC", y = "iPS", data = df.cuff, d.factor = NULL, type = "cuffdiff", title = TRUE, grid = TRUE, highlight = hl ) # Extract data frame from visualization data("df.cuff") tmp <- vsScatterPlot( x = "hESC", y = "iPS", data = df.cuff, d.factor = NULL, type = "cuffdiff", title = TRUE, grid = TRUE, data.return = TRUE ) df_scatter <- tmp[[1]] ## or use tmp$data head(df_scatter) # Show plot from object (see prior example for more details) tmp[[2]] ## or use tmp$plot