View source: R/Spatial_module_expression.R
Spatial_module_expression | R Documentation |
Plotting the expression of a gene module on the spatial image with or without a threshold.
Spatial_module_expression( sample_names, gene.set, GEX.out.directory.list, bcs_merge, images_tibble, title, size, threshold, legend_title )
sample_names |
Character vector containing the name of the sample. |
gene.set |
Charcter vector containing the markers name. |
GEX.out.directory.list |
Character vector that give the path to filtered_feature_bc_matrix data. |
bcs_merge |
Data frame containing imagerow, imagecol and barcode of the cells belonging to the spatial image. It can also be created by the function scaling_spatial_image_parameter by selecting the output parameter 10. |
images_tibble |
Tbl-df containing the sample name, grob, height and width of the spatial image. It can also be created by the function scaling_spatial_image_parameter by selecting the output parameter 5. |
title |
Character vector to name the plot. |
size |
Number, to define the size of the text, default = 15. |
threshold |
Number, to define the threshold. If threshold = No, plot of the module and if threshold is a number, plot show the cells above the threshold. |
legend_title |
Character vector to name the legend scale. |
Returns a ggplot of gene module expression.
## Not run: gene.set <- list() # make empty list gene.set[[1]] <- c("CD19","XBP1","SDC1") # put gene set in list #Without expression threshold Spatial_module_expression(sample_names = sample_names,gene.set = gene.set, GEX.out.directory.list = GEX.out.directory.list[[1]],bcs_merge = scaling_parameters[[10]], images_tibble = scaling_parameters[[5]], threshold = "No") #With expression threshold Spatial_module_expression(sample_names = sample_names,gene.set = gene.set, GEX.out.directory.list = GEX.out.directory.list[[1]],bcs_merge = scaling_parameters[[10]], images_tibble = scaling_parameters[[5]], threshold = 1) ## End(Not run)
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