View source: R/format_cellprofiler_to_spe.R
format_cellprofiler_to_spe | R Documentation |
Reads in spatial data in the form of cell coordinates, cell phenotypes (if available), and marker intensities and transforms to a SpatialExperiment object. The assay stores the intensity level of every marker (rows) for every cell (columns). Cell phenotype is stored under 'colData()'. Cell x and y coordinates are stored under 'spatialCoords()' Note that if the data does not include these parameters, we recommend adding it to the output from cellprofiler with NAs in columns.
format_cellprofiler_to_spe(
path = NULL,
markers = NULL,
intensity_columns_interest = NULL
)
path |
String of the path location cellprofiler csv file. |
markers |
String Vector containing the markers used for staining. |
intensity_columns_interest |
String Vector with the names of the columns with the level of each marker. Column names must match the order of the 'markers' parameter. |
Note when specifying 'markers', please use "DAPI" to replace "DNA" due to implementation. The output data will include "DAPI" instead of "DNA".
A SpatialExperiment object is returned
path <- system.file("extdata", "tiny_cellprofiler.txt.gz", package = "SPIAT")
markers <- c("Marker1", "Marker2", "Marker3", "Marker4", "Marker5", "DAPI",
"Marker6")
intensity_columns_interest <- c("Intensity_MeanIntensity_Marker1_rs",
"Intensity_MeanIntensity_Marker2_rs", "Intensity_MeanIntensity_Marker3_rs",
"Intensity_MeanIntensity_Marker4_rs", "Intensity_MeanIntensity_Marker5_rs",
"Intensity_MeanIntensity_DAPI_rs", "Intensity_MeanIntensity_Marker6_rs")
formatted_cellprofiler <- format_cellprofiler_to_spe(path = path,
markers = markers, intensity_columns_interest = intensity_columns_interest)
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