View source: R/Script_DROPLET_07_ADHOC_PLOT_PCA_1_PlotFeatures.R
PlotValues.PCA.CellGroup.10x | R Documentation |
Annotates reduced dimension space, e.g., UMAP and tSNE, with cell features such as cell group, donor ID, sample ID, etc.
PlotValues.PCA.CellGroup.10x( MarvelObject, cell.group.list, legendtitle = "Cell group", alpha = 0.75, point.size = 1, point.stroke = 0.1, point.colors = NULL, point.size.legend = 2, type )
MarvelObject |
Marvel object. S3 object generated from |
cell.group.list |
List of character strings. Each element of the list is a vector of cell IDs corresponding to a feature, e.g. cell group. The names of the element will be the cell feature label. |
legendtitle |
Character string. Legend title. Default is |
alpha |
Numeric value. Transparency of the data points. Takes any values between 0-1 whereby 0 is totally transparent and 1 is opaque. Default is |
point.size |
Numeric value. Size of data points. Default is |
point.stroke |
Numeric value. Outline thickness of data points. Default is |
point.colors |
Vector of character strings. Colors of cell groups and should be same length as |
point.size.legend |
Numeric value. Size of legend keys. Default is |
type |
Character string. Type of reduced dimension space. Options are |
An object of class S3 with new slot MarvelObject$adhocPlot$PCA$CellGroup
.
marvel.demo.10x <- readRDS(system.file("extdata/data", "marvel.demo.10x.rds", package="MARVEL") ) # Define cell groups # Retrieve sample metadata sample.metadata <- marvel.demo.10x$sample.metadata # iPSC index <- which(sample.metadata$cell.type=="iPSC") cell.ids.1 <- sample.metadata[index, "cell.id"] length(cell.ids.1) # Cardio day 10 index <- which(sample.metadata$cell.type=="Cardio day 10") cell.ids.2 <- sample.metadata[index, "cell.id"] length(cell.ids.2) # Save into list cell.group.list <- list("iPSC"=cell.ids.1, "Cardio d10"=cell.ids.2 ) # Plot cell groups marvel.demo.10x <- PlotValues.PCA.CellGroup.10x( MarvelObject=marvel.demo.10x, cell.group.list=cell.group.list, legendtitle="Cell group", type="tsne" ) # Check output marvel.demo.10x$adhocPlot$PCA$CellGroup
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.