Open GODCALLMEGOD opened 5 months ago
Dear authors: I have little idea of the workflow. Just writing to ask you a favor. Here's my codes,if there is any mistake?
`xyz <- read.csv('./spatial/tissue_positions_list.csv', header = FALSE, col.names = c( "barcode", "in_tissue", "array_row", "array_col", "pxl_row_in_fullres", "pxl_col_in_fullres")) exp<-DropletUtils::read10xCounts('GSM6433593_094C_filtered_feature_bc_matrix.h5',type = 'HDF5',row.names = 'symbol') rd <- S4Vectors::DataFrame( symbol = rowData(exp)$Symbol) xz<-xyz[!xyz$in_tissue=='0',] st <- SpatialExperiment( assays = list(counts = assay(exp)), rowData = rd, colData = DataFrame(xz), spatialCoordsNames = c("pxl_col_in_fullres", "pxl_row_in_fullres"), imgData = img, sample_id = "sample01")
res <- SPOTlight( x = sce, y = st, groups = as.character(sce$celltype_minor), # 也可以是cluster mgs = mgs_df, hvg = hvg, weight_id = "mean.AUC", group_id = "cluster", gene_id = "gene")
head(mat <- res$mat)[, seq_len(length(unique(sce$celltype_minor)))] mod <- res$NMF
p3 <- plotSpatialScatterpie( x = st, y = mat, cell_types = colnames(mat), img = T, #以tiff为背景 scatterpie_alpha = 1, pie_scale = 0.4,
degrees = -90,
axis = "h") + scale_fill_manual( values = pal, breaks = names(pal))`
Dear authors: I have little idea of the workflow. Just writing to ask you a favor.
Here's my codes,if there is any mistake?
`xyz <- read.csv('./spatial/tissue_positions_list.csv', header = FALSE, col.names = c( "barcode", "in_tissue", "array_row", "array_col", "pxl_row_in_fullres", "pxl_col_in_fullres")) exp<-DropletUtils::read10xCounts('GSM6433593_094C_filtered_feature_bc_matrix.h5',type = 'HDF5',row.names = 'symbol') rd <- S4Vectors::DataFrame( symbol = rowData(exp)$Symbol) xz<-xyz[!xyz$in_tissue=='0',] st <- SpatialExperiment( assays = list(counts = assay(exp)), rowData = rd, colData = DataFrame(xz), spatialCoordsNames = c("pxl_col_in_fullres", "pxl_row_in_fullres"), imgData = img, sample_id = "sample01")
res <- SPOTlight( x = sce, y = st, groups = as.character(sce$celltype_minor), # 也可以是cluster mgs = mgs_df, hvg = hvg, weight_id = "mean.AUC", group_id = "cluster", gene_id = "gene")
head(mat <- res$mat)[, seq_len(length(unique(sce$celltype_minor)))] mod <- res$NMF
p3 <- plotSpatialScatterpie( x = st, y = mat, cell_types = colnames(mat), img = T, #以tiff为背景 scatterpie_alpha = 1, pie_scale = 0.4,
Rotate the image 90 degrees counterclockwise
degrees = -90,
Pivot the image on its x axis
axis = "h") + scale_fill_manual( values = pal, breaks = names(pal))`