Hi, I am pretty new to the Squidpy. please excuse me with my naive questions.
I have a codex outputs a CSV files but i am not sure how to load the csv files or which tutorial I should follow .
In surate I can use this code to load
codex.obj <- LoadAkoya(filename = "LN7910_20_008_11022020_reg001_compensated.csv", type = "processor", fov = "HBM754.WKLP.262") codex.obj <- NormalizeData(object = codex.obj, normalization.method = "CLR", margin = 2) codex.obj <- ScaleData(codex.obj) VariableFeatures(codex.obj) <- rownames(codex.obj) # since the panel is small, treat all features as variable. codex.obj <- RunPCA(object = codex.obj, npcs = 20, verbose = FALSE) codex.obj <- RunUMAP(object = codex.obj, dims = 1:20, verbose = FALSE) codex.obj <- FindNeighbors(object = codex.obj, dims = 1:20, verbose = FALSE) codex.obj <- FindClusters(object = codex.obj, verbose = FALSE, resolution = 0.4, n.start = 1)
Thanks for your helps