vsBoxPlot {vidger} | R Documentation |
This function allows you to extract necessary results-based data from analytical objects to create a box plot comparing log10(FPKM or CPM) distributions for experimental treatments.
vsBoxPlot(data, d.factor = NULL, type = c("cuffdiff", "deseq", "edger"), title = TRUE, legend = TRUE, grid = TRUE, aes = c("box", "violin", "boxdot", "viodot", "viosumm", "notch"), fill.color = NULL, data.return = FALSE, xaxis.text.size = 10, yaxis.text.size = 10, xaxis.title.size = 12, yaxis.title.size = 12, main.title.size = 15, legend.text.size = 10, legend.title.size = 12)
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
|
legend |
display legend of plot. Logical; defaults to |
grid |
display major and minor axis lines. Logical; defaults to
|
aes |
changes overall layout of the graph. |
fill.color |
changes the fill color for the plots. See
|
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 |
legend.text.size |
change the font size of the legend body text.
Defaults to |
legend.title.size |
change the font size of the legend title text.
Defaults to |
An object created by ggplot
Brandon Monier, brandon.monier@sdstate.edu
# Cuffdiff example data("df.cuff") vsBoxPlot( data = df.cuff, d.factor = NULL, type = "cuffdiff", title = TRUE, legend = TRUE, grid = TRUE ) # DESeq2 example data("df.deseq") require(DESeq2) vsBoxPlot( data = df.deseq, d.factor = "condition", type = "deseq", title = TRUE, legend = TRUE, grid = TRUE ) # edgeR example data("df.edger") require(edgeR) vsBoxPlot( data = df.edger, d.factor = NULL, type = "edger", title = TRUE, legend = TRUE, grid = TRUE ) # Display different colors for plot data("df.edger") vsBoxPlot( data = df.edger, d.factor = NULL, type = "edger", title = TRUE, legend = TRUE, grid = TRUE, fill.color = "RdGy", data.return = FALSE ) # Extract data frame from visualization data("df.edger") require(edgeR) tmp <- vsBoxPlot( data = df.edger, d.factor = NULL, type = "edger", title = TRUE, legend = TRUE, grid = TRUE, data.return = FALSE ) df_box <- tmp[[1]] ## or use tmp$data head(df_box) # Show plot from object (see prior example for more details) tmp[[2]] ## or use tmp$plot