clust.stats.plot {iCellR} | R Documentation |
This function takes an object of class iCellR and creates QC plot.
clust.stats.plot( x = NULL, plot.type = "box.mito", conds.to.plot = NULL, cell.color = "slategray3", cell.size = 1, cell.transparency = 0.5, box.color = "red", box.line.col = "green", back.col = "white", notch = FALSE, interactive = TRUE, out.name = "plot" )
x |
An object of class iCellR. |
plot.type |
Choose from "bar.cc", "pie.cc" , box.umi", "box.mito", "box.gene", default = "box.mito". |
conds.to.plot |
Choose the conditions you want to see in the plot, default = NULL (all conditions). |
cell.color |
Choose a color for points in the plot. |
cell.size |
A number for the size of the points in the plot, default = 1. |
cell.transparency |
Color transparency for points in "scatterplot" and "boxplot", default = 0.5. |
box.color |
A color for the boxes in the "boxplot", default = "red". |
box.line.col |
A color for the lines around the "boxplot", default = "green". |
back.col |
Background color, default = "white" |
notch |
Notch the box plots, default = FALSE. |
interactive |
If set to TRUE an interactive HTML file will be created, default = TRUE. |
out.name |
If "interactive" is set to TRUE, the out put name for HTML, default = "plot". |
An object of class iCellR.
clust.stats.plot(demo.obj, plot.type = "box.mito", interactive = FALSE, out.name = "box.mito.clusters")