cluster.plot {iCellR} | R Documentation |
Plot nGenes, UMIs and perecent mito
Description
This function takes an object of class iCellR and creates plots to see the clusters.
Usage
cluster.plot(
x = NULL,
cell.size = 0.5,
plot.type = "tsne",
cell.color = "black",
back.col = "white",
col.by = "clusters",
cond.facet = FALSE,
cond.shape = FALSE,
anno.clust = FALSE,
anno.size = 4,
cell.transparency = 1,
clust.dim = 2,
angle = 20,
clonotype.max = 10,
density = FALSE,
interactive = TRUE,
static3D = FALSE,
out.name = "plot"
)
Arguments
x |
An object of class iCellR. |
cell.size |
A numeric value for the size of the cells, default = 1. |
plot.type |
Choose between "tsne", "pca", "umap", "knetl", "diffusion", default = "tsne". |
cell.color |
Choose cell color if col.by = "monochrome", default = "black". |
back.col |
Choose background color, default = "black". |
col.by |
Choose between "clusters", "conditions", "cc" (cell cycle) or "monochrome", default = "clusters". |
cond.facet |
Show the conditions in separate plots. |
cond.shape |
If TRUE the conditions will be shown in shapes. |
anno.clust |
Annotate cluster names on the plot, default = TRUE. |
anno.size |
If anno.clust is TRUE set font size, default = 3. |
cell.transparency |
A numeric value between 0 to 1, default = 0.5. |
clust.dim |
A numeric value for plot dimensions. Choose either 2 or 3, default = 2. |
angle |
A number to rotate the non-interactive 3D plot. |
clonotype.max |
Number of clonotype to plot, default = 10. |
density |
If TRUE the density plots for PCA/tSNE second dimension will be created, default = FALSE. |
interactive |
If TRUE an html interactive file will be made, default = TRUE. |
static3D |
If TRUE a non-interactive 3D plot will be made. |
out.name |
Output name for html file if interactive = TRUE, default = "plot". |
Value
An object of class iCellR.