View source: R/initiateSpataObject.R
initiateSpataObject_CountMtr | R Documentation |
spata2
object from a raw count matrixDefault function for any spatial related experiment whoose spata2
objects are initiated with
a raw count matrix. See details for more information.
initiateSpataObject_CountMtr(
coords_df,
count_mtr,
sample_name,
spatial_method = "Unknown",
image = NULL,
image_class = "HistologyImage",
image_object = NULL,
feature_df = NULL,
directory_spata = NULL,
directory_seurat = NULL,
combine_with_wd = FALSE,
SCTransform = FALSE,
NormalizeData = list(normalization.method = "LogNormalize", scale.factor = 1000),
FindVariableFeatures = list(selection.method = "vst", nfeatures = 2000),
ScaleData = TRUE,
RunPCA = list(npcs = 60),
FindNeighbors = list(dims = 1:30),
FindClusters = list(resolution = 0.8),
RunTSNE = TRUE,
RunUMAP = list(dims = 1:30),
verbose = TRUE,
...
)
coords_df |
Data.frame containing information about the positions of all barcode-spots in form of a numeric x- and y-variable. The key-variable barcodes needs to be of type character and must be identical to the column names of the input matrix. |
count_mtr |
A numeric matrix to be used as the count matrix. Rownames must correspond to the genes and column names must correspond to the barcodes. |
sample_name |
Character value. Denotes the name of the sample you are
analyzing with the spata-object. The future input for SPATA's |
image |
An Image of the sample that can be displayed as the surface plot's background. |
SCTransform |
A named list of arguments given to |
NormalizeData |
A named list of arguments given to |
FindVariableFeatures |
A named list of arguments given to |
ScaleData |
A named list of arguments given to Hint: If set to TRUE or the argument-list provided does not specify the argument |
RunPCA |
A named list of arguments given to |
FindNeighbors |
A named list of arguments given to |
FindClusters |
A named list of arguments given to |
RunTSNE |
A named list of arguments given to |
RunUMAP |
A named list of arguments given to |
... |
Additional parameters given to |
The loading and preprocessing of the spata2
object currently relies on the Seurat-package. Before any pre processing function is applied
mitochondrial and stress genes are discarded. For more advanced users the arguments above starting with a capital letter allow to
manipulate the way the spata2
object is processed. For all of these arguments apply the following instructions:
If set to FALSE the processing function is skipped.
If set to TRUE the respective function is called with it's default argument settings. Note: RunUMAP()
needs
additional input!
If a named list is provided the respective function is called whereby the named list will provide the argument-input (the Seurat
object to be constructed must not be named and will be
passed to every function as the first argument!!!.)
Note that certain listed functions require previous functions! E.g. if RunPCA
is set to FALSE RunTSNE()
will result in an error. (base::tryCatch()
will prevent the function from crashing but the respective slot
is going to be empty.) Skipping functions might result in an incomplete spata2
object.
A spata2
object.
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