cluster.plot {iCellR} | R Documentation |
This function takes an object of class iCellR and creates plots to see the clusters.
cluster.plot( x = NULL, cell.size = 1, 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 = 0.5, clust.dim = 2, angle = 20, clonotype.max = 10, density = FALSE, interactive = TRUE, static3D = FALSE, out.name = "plot" )
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". |
An object of class iCellR.
cluster.plot(demo.obj,plot.type = "umap",interactive = FALSE) cluster.plot(demo.obj,plot.type = "tsne",interactive = FALSE) cluster.plot(demo.obj,plot.type = "pca",interactive = FALSE) cluster.plot(demo.obj,plot.type = "pca",col.by = "conditions",interactive = FALSE) cluster.plot(demo.obj,plot.type = "umap",col.by = "conditions",interactive = FALSE) cluster.plot(demo.obj,plot.type = "tsne",col.by = "conditions",interactive = FALSE)