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 |
output generated from calling the main routines of either 'cuffdiff', 'DESeq2', or 'edgeR' analyses. For 'cuffdiff', this will be a '*_exp.diff' file. For 'DESeq2', this will be a generated object of class 'DESeqDataSet'. For 'edgeR', this will be a generated object of class 'DGEList'. |
d.factor |
a specified factor; for use with 'DESeq2' objects only. This input equates to the first parameter for the contrast argument when invoking the 'results()' function in 'DESeq2'. Defaults to 'NULL'. |
type |
an analysis classifier to tell the function how to process the data. Must be either 'cuffdiff', 'deseq', or 'edger'. 'cuffdiff' must be used with 'cuffdiff' data; 'deseq' must be used for 'DESeq2' output; 'edgeR' must be used with 'edgeR' data. See the 'data' parameter for further details. |
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 'NULL'. |
title |
display the main title of plot. Logical; defaults to 'TRUE'. If set to 'FALSE', no title will display in plot. |
grid |
display major and minor axis lines. Logical; defaults to 'TRUE'. If set to 'FALSE', no axis lines will display in plot. |
man.title |
a manually specified title at the authors discretion. Defaults to 'NULL'. |
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 )