View source: R/Spatial_marker_expression.R
Spatial_marker_expression | R Documentation |
Plotting a gene of interest in selected cells on the spatial image.
Spatial_marker_expression( sample_names, bcs_merge, images_tibble, matrix, marker, GEX_barcode, title, threshold, size )
sample_names |
Character vector containing the name of the sample. |
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. |
matrix |
Data frame containing all the genes detected per cells. This data frame can be obtained by the scaling_parameters functions. |
marker |
Character vector containing the name of a gene of interest. |
GEX_barcode |
Character vector containing the GEX barcode of the cell of interest with the -1 at the end |
title |
Character vector to name the plot. |
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. |
size |
Number, to define the size of the text, default = 15. |
Returns a plot of the level of expression of a gene in cells.
## Not run: GEX_BCR_barcode<-vgm_with_simulated_VDJ$VDJ$GEX_barcode GEX_BCR_barcode<-paste0(GEX_BCR_barcode,"-1") #Add -1 at the end of each barcode #Without expression threshold Spatial_marker_expression(matrix=scaling_parameters[[9]], marker="CD3E",bcs_merge=scaling_parameters[[10]], images_tibble=scaling_parameters[[5]], GEX_barcode=GEX_BCR_barcode,sample_names=sample_names, title = "B cells", threshold = "No") #With expression threshold Spatial_marker_expression(matrix=scaling_parameters[[9]], marker="CD3E",bcs_merge=scaling_parameters[[10]], images_tibble=scaling_parameters[[5]], GEX_barcode=GEX_BCR_barcode,sample_names=sample_names, title = "B cells", threshold = 5) ## End(Not run)
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