vsScatterMatrix {vidger} | R Documentation |
This function will generate a matrix of scatterplots for all possible treatment combinations with additional distribution info.
vsScatterMatrix(data, d.factor = NULL, type = c("cuffdiff", "deseq", "edger"), comp = NULL, title = TRUE, grid = TRUE, man.title = NULL, data.return = FALSE, xaxis.text.size = 9, yaxis.text.size = 9, xaxis.title.size = 10, yaxis.title.size = 10, main.title.size = 15, facet.title.size = 10)
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 |
comp |
treatments you would like to compare in the form of a vector.
If no parameter is specified, all possible treatment comparisons will be
made. Defaults to |
title |
display the main title of plot. Logical; defaults to
|
grid |
display major and minor axis lines. Logical; defaults to
|
man.title |
a manually specified title at the authors discretion.
Defaults 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 |
facet.title.size |
change the font size of the facet wrap title text.
Defaults to |
An object created by ggplot
Brandon Monier, brandon.monier@sdstate.edu
# Cuffdiff example data("df.cuff") vsScatterMatrix( data = df.cuff, d.factor = NULL, type = "cuffdiff", comp = NULL, title = TRUE, grid = TRUE, man.title = "Example title" ) # DESeq2 example data("df.deseq") require(DESeq2) vsScatterMatrix( data = df.deseq, d.factor = "condition", type = "deseq", comp = NULL, title = TRUE, grid = FALSE, man.title = NULL ) # edgeR example data("df.edger") require(edgeR) vsScatterMatrix( data = df.edger, d.factor = NULL, type = "edger", comp = c("WM", "MM"), title = TRUE, grid = TRUE, man.title = NULL ) # Extract data frame from visualization data("df.edger") tmp <- vsScatterMatrix( data = df.edger, d.factor = NULL, type = "edger", comp = c("WM", "MM"), title = TRUE, grid = TRUE, man.title = NULL, data.return = TRUE ) df_scatmat <- tmp[[1]] ## or use tmp$data head(df_scatmat) # Show plot from object (see prior example for more details) tmp[[2]] ## or use tmp$plot