GRN
objectplotGeneralGraphStats.Rd
This function generates graphical summaries about the structure and connectivity of the TF-peak-gene and TF-gene graphs. These include, distribution of vertex types (TF, peak, gene) and edge types (tf-peak, peak-gene), the distribution of vertex degrees, and the most "important" vertices according to degree centrality and eigenvector centrality scores.
plotGeneralGraphStats(
GRN,
outputFolder = NULL,
basenameOutput = NULL,
plotAsPDF = TRUE,
pdf_width = 12,
pdf_height = 12,
pages = NULL,
forceRerun = FALSE
)
Object of class GRN
Character or NULL
. Default NULL
. If set to NULL
, the default output folder as specified when initiating the
object in initializeGRN
will be used. Otherwise, all output from this function will be put into the specified folder.
If a folder is provided, while we recommend specifying an absolute path, a relative one also works.
NULL
or character. Default NULL
. Basename of the output files that are produced. If set to NULL
, a default basename is chosen. If a custom basename is specified, all output files will have the chosen basename as file prefix, be careful with not overwriting already existing files (if forceRerun
is set to TRUE
)
TRUE
or FALSE
. Default TRUE
.Should the plots be printed to a PDF file? If set to TRUE
, a PDF file is generated, the name of which depends on the value of basenameOutput
. If set to FALSE
, all plots are printed to the currently active device. Note that most functions print more than one plot, which means you may only see the last plot depending on your active graphics device.
Number>0. Default 12. Width of the PDF, in cm.
Number >0. Default 12. Height of the PDF, in cm.
Integer vector or NULL
. Default NULL
. Page number(s) to plot. Can be used to plot only specific pages to a PDF or the currently active graphics device.
TRUE
or FALSE
. Default FALSE
. Force execution, even if the GRN object already contains the result. Overwrites the old results.
The same GRN
object, without modifications.
# See the Workflow vignette on the GRaNIE website for examples
GRN = loadExampleObject()
#> Downloading GRaNIE example object from https://git.embl.de/grp-zaugg/GRaNIE/-/raw/master/data/GRN.rds
#> Finished successfully. You may explore the example object. Start by typing the object name to the console to see a summaty. Happy GRaNIE'ing!
GRN = plotGeneralGraphStats(GRN, plotAsPDF = FALSE, pages = 1)
#> INFO [2024-09-25 19:18:48] Plotting directly
#> INFO [2024-09-25 19:18:48] Finished successfully. Execution time: 0.8 secs