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theMILOlab / SPATA2

A Toolbox for Spatial Transcriptomics Analysis
https://themilolab.github.io/SPATA2/
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error in runAutoencoderDenoising #145

Open renyzh5 opened 3 months ago

renyzh5 commented 3 months ago

seurat_object <- Seurat::SCTransform(seurat_object, assay = "Spatial", verbose = FALSE) Seurat::SpatialFeaturePlot(seurat_object, features = c("nCount_Spatial"))

spata_obj <- SPATA2::asSPATA2( object = seurat_object, sample_name = "P15T", image_name = "image_P15_T", spatial_method = "Visium" )

######################### #########################

all expression matrices before denoising

getExpressionMatrixNames(object = spata_obj) [1] "scaled"

active expression matrix before denoising

getActiveMatrixName(object = spata_obj) 16:29:26 Using matrix 'counts'. [1] "counts"

denoising your data

spata_obj <- runAutoencoderDenoising( object = spata_obj, activation = "selu", bottleneck = 56, epochs = 20, layers = c(128, 64, 32), dropout = 0.1 )

Checking input for validity. Error in UseMethod("compile") : no applicable method for 'compile' applied to an object of class "c('keras.src.models.functional.Functional', 'keras.models.functional.Functional', 'keras.src.ops.function.Function', 'keras.ops.function.Function', 'keras.src.models.model.Model', 'keras.models.model.Model', 'keras.src.backend.tensorflow.trainer.TensorFlowTrainer', 'keras.backend.tensorflow.trainer.TensorFlowTrainer', 'keras.src.trainers.trainer.Trainer', 'keras.trainers.trainer.Trainer', 'keras.src.layers.layer.Layer', 'keras.layers.layer.Layer', 'keras.src.backend.tensorflow.layer.TFLayer', 'keras.backend.tensorflow.layer.TFLayer', 'keras.src.backend.tensorflow.trackable.KerasAutoTrackable', 'keras.backend.tensorflow.trackable.KerasAutoTrackable', 'tensorflow.python.trackable.autotrackable.AutoTrackable', 'tensorflow.python.trackable.base.Trackable', 'keras.src.ops.operation.Operation', 'keras.ops.operation.Operation', 'keras.src.saving.keras_saveable.KerasSaveable', 'keras.saving.keras_saveable.KerasSaveable' In addition: Warning message: In confuns::give_feedback(msg = msg, fdb.fn = fdb_fn, with.time = FALSE) : Argument of_sample is deprecated and no longer in use.( used by runAutoencoderDenoising() )

how can I solve this problem? thank you!

kueckelj commented 2 months ago

Hello renyzh5, sorry for the late reply. The autoencoder functions are currently under supervision. They will be exported in upcoming version releases again.

hlcxq1223 commented 2 months ago

Hello renyzh5, sorry for the late reply. The autoencoder functions are currently under supervision. They will be exported in upcoming version releases again.

Hello kueckelj, did the autoencoder functions remain in the SPATA2 3.0 version? I can't find them in the tutorial.

kueckelj commented 2 months ago

You won't find them right now cause I did not export them. I have to adjust the functions to the new version which I have not done yet. It is on my to-do list for the next days but I can not be precise about when I upload them. I will let you know!

Jianbo1999 commented 1 week ago

What's happen? X98 <-