plotAssemblyStats {ngsReports} | R Documentation |
Plot a summary of assembly stats from a set of log files
plotAssemblyStats( x, type = c("quast", "busco"), usePlotly = FALSE, plotType = c("bar", "paracoord"), ... )
x |
Paths to one or more log files |
type |
The tool used. Can be one of quast or busco |
usePlotly |
logical. If TRUE an interactive plot will be generated. If FALSE a ggplot object will be output |
plotType |
|
... |
Used to pass additional attributes to theme() and between methods |
Loads a set of assembly log files and creates a default plot.
Implemented tools are quast
and BUSCO
.
quast will plot a parralel coordinate plot of some assembly statistics
BUSCO will plot a stacked barplot of completeness statistics
A ggplot2 object, or a plotly object
#getquast log filenames quastFiles <- system.file("extdata", c("quast1.tsv", "quast2.tsv"), package = "ngsReports") # The default plot plotAssemblyStats(quastFiles)