UpSet plot for Domain Architectures vs Domains and Genomic Contexts vs Domain Architectures.
Usage
plotUpSet(
query_data = "toast_rack.sub",
colname = "DomArch",
cutoff = 90,
RowsCutoff = FALSE,
text.scale = 1.5,
point.size = 2.2,
line.size = 0.8
)Arguments
- query_data
Data frame of protein homologs with the usual 11 columns + additional word columns (0/1 format). Default is toast_rack.sub
- colname
Column name from query_data: "DomArch.norep", "GenContext.norep", "DomArch.PFAM.norep" or "DomArch.LADB.norep". Default is "DomArch.norep".
- cutoff
Numeric. Cutoff for word frequency. Default is 90.
- RowsCutoff
Boolean. If TRUE, applies a row cutoff to remove data rows based on a certain condition. Default is FALSE.
- text.scale
Allows scaling of axis title, tick lables, and numbers above the intersection size bars. text.scale can either take a universal scale in the form of an integer, or a vector of specific scales in the format: c(intersection size title, intersection size tick labels, set size title, set size tick labels, set names, numbers above bars)
- point.size
Numeric. Sets the size of points in the UpSet plot. Default is 2.2.
- line.size
Numeric. Sets the line width in the UpSet plot. Default is 0.8.
Value
An UpSet plot object. The plot visualizes intersections of sets based on the provided colname in query_data.