Combine Nanostring Digital Spatial Profile read count and annotation files into a GeoMX object
studyDesign(
dcc.files,
pkc.files,
pheno.data.file,
pheno.data.sheet = "Template",
pheno.data.dcc.col.name = "Sample_ID",
protocol.data.col.names = c("aoi", "roi"),
experiment.data.col.names = c("panel"),
slide.name.col = "slide name",
class.col = "class",
region.col = "region",
segment.col = "segment",
area.col = "area",
nuclei.col = "nuclei",
sankey.exclude.slide = FALSE,
segment.id.length = 4
)A character vector containing the paths to the DCC files.
A character vector representing the path to the corresponding PKC file
An optional character string representing the path to the corresponding phenotypic excel data file. It is recommended to use the Lab Worksheet in the exact order samples are provided in.
An optional character string representing the excel sheet name containing the phenotypic data.
Character string identifying unique sample identifier column in phenoDataFile.
Character list of column names from phenoDataFile containing data about the experimental protocol or sequencing data.
Character list of column names from phenoDataFile containing data about the experiment's meta-data.
The name of the field that contains the slide names
The name of the field that contains the class annotation
The name of the field that contains the region annotation
The name of the field that contains the segment name
The name of the field that contains the segment area
The name of the field that contains the nuclei number
A toggle for including the slide name in the Sankey plot
The number of characters to use from each of the annotation fields class, region, and segment to create the segment ID
A list containing the NanoString Object and the Sankey plot.
studyDesign returns a Sankey Plot and a GeoMX object.
For the function to run properly the annotation excel file must have the
specific field names: slide name', class, segment, region
and the corresponding fields that can be renamed: Sample_ID, aoi, roi, panel