visualiseWSIRDirections

A function to easily visualise the low-dimensional gene expression data. This function plots each cell at its true spatial coordinates, coloured by their values for WSIR1 / WSIR2 / ... . The plots give an intuition about what biological signals are contained in the WSIR directions.

Usage

visualiseWSIRDirections(
  coords,
  WSIR,
  dirs = 6,
  mincol = "blue",
  maxcol = "red"
)

Arguments

coords

dataframe containing spatial positions of n cells in 2D space. Dimension n * 2. Column names must be c("x", "y").

WSIR

wsir object as output of wSIR function. To analyse a different DR method, ensure the slot named 'directions' contains the loadings as a matrix with the gene names as the rownames. Must have used the same coords parameter as in coords parameter for this function.

dirs

integer for how many of the low-dimensional directions you would like to visualise. Recommend no more than 10 for ease of visualisation. Default is 6.

mincol

String for the colour of low values of low-dimensional directions. Personal choice for user, default is "blue".

maxcol

String for the colour of high values of low-dimensional directions. Personal choice for user, default is "red".

Value

Grid of plots with dirs number of plots. Each shows the cells at their spatial positions coloured by their value for each of the first 'dirs' WSIR directions.

Examples

data(MouseData)
wsir_obj = wSIR(X = sample1_exprs,
  coords = sample1_coords,
  optim_params = FALSE,
  alpha = 4,
  slices = 6) # create wsir object
vis_obj = visualiseWSIRDirections(coords = sample1_coords,
WSIR = wsir_obj, dirs = 8) # create visualisations
vis_obj