3 clusterCornerAxes

clusterCornerAxes is used to add corner axis on the left-bottom UMAP/tSNE principle component plot.

3.1 load test data

We load test data in scRNAtoolVis package:

library(scRNAtoolVis)

# load test data
test <- system.file("extdata", "seuratTest.RDS", package = "scRNAtoolVis")
tmp <- readRDS(test)

3.2 examples

default plot:

# umap
clusterCornerAxes(object = tmp,reduction = 'umap',
                  noSplit = T)

We can change arrow type:

# arrowType
clusterCornerAxes(object = tmp,reduction = 'umap',
                  noSplit = T,arrowType = 'open')

We can facet by seurat metadata column catogary variable:

# facet by metadata column "orig.ident"
clusterCornerAxes(object = tmp,
                  reduction = 'umap',
                  noSplit = F,
                  groupFacet = 'orig.ident',
                  aspect.ratio = 1,
                  relLength = 0.5)

If multiple corner axises will confuse you, you can also set axes = ‘one’ to retain only one axis on the left:

# retain only one axes
clusterCornerAxes(object = tmp,
                  reduction = 'umap',
                  noSplit = F,
                  groupFacet = 'orig.ident',
                  aspect.ratio = 1,
                  relLength = 0.5,
                  axes = 'one')

Change the axis and label color:

# line color
clusterCornerAxes(object = tmp,
                  reduction = 'umap',
                  noSplit = F,
                  groupFacet = 'orig.ident',
                  aspect.ratio = 1,
                  relLength = 0.5,
                  lineTextcol = 'grey50')

Use tSNE reduction data:

# tsne
clusterCornerAxes(object = tmp,
                  reduction = 'tsne',
                  noSplit = F,
                  groupFacet = 'orig.ident',
                  aspect.ratio = 1,
                  relLength = 0.5)

Change a cool theme:

clusterCornerAxes(object = tmp,
                  reduction = 'umap',
                  noSplit = F,
                  groupFacet = 'orig.ident',
                  aspect.ratio = 1,
                  relLength = 0.5,
                  cornerTextSize = 2,
                  themebg = 'bwCorner')

You can set the keySize to change legend size:

# legend key size
clusterCornerAxes(object = tmp,
                  reduction = 'umap',
                  clusterCol = 'cellType',
                  noSplit = T,
                  keySize = 8)

Add cellType names in plot:

# add cell type
clusterCornerAxes(object = tmp,
                  reduction = 'umap',
                  clusterCol = "cellType",
                  noSplit = T,
                  cellLabel = T,
                  cellLabelSize = 5)

Remove legend:

# remove legend
clusterCornerAxes(object = tmp,
                  reduction = 'umap',
                  clusterCol = "cellType",
                  noSplit = T,
                  cellLabel = T,
                  cellLabelSize = 5,
                  show.legend = F)

Split by group:

# split
clusterCornerAxes(object = tmp,
                  reduction = 'umap',
                  clusterCol = "cellType",
                  groupFacet = 'orig.ident',
                  noSplit = F,
                  cellLabel = T,
                  cellLabelSize = 3,
                  show.legend = F,
                  aspect.ratio = 1,
                  themebg = 'bwCorner')

3.3 add circle

You can add circles to each clusters to mark:

# add circle
clusterCornerAxes(object = tmp,reduction = 'umap',
                  noSplit = T,
                  cornerTextSize = 3.5,
                  themebg = 'bwCorner',
                  addCircle = TRUE,
                  cicAlpha = 0.2,
                  nbin = 200)

Relative parameters to control the circle as follows: