add_paraview {mistyR} | R Documentation |
The paraview captures the expression of all markers in the broader tissue structure.
add_paraview( current.views, positions, l, approx = 1, nn = NULL, cached = FALSE, verbose = TRUE )
current.views |
the current view composition. |
positions |
a |
l |
effective radius of influence of expression in the broader tissue structure. |
approx |
rank of the Nyström approximation matrix. (see Details) |
nn |
the number of spatial units to be used for approximating the paraview using a fast nearest neighbor search. (see Details) |
cached |
a |
verbose |
a |
The paraview is generated by weighted sum of the expression of all spatial
units for each marker. The weights for each spatial unit i are dependent
on the distance to the spatial unit j and the parameter l
and are
calculated using the radial basis function
w(i,j) = exp(-d(i,j)^2/l^2)
Since the generation of the paraview requires the calculation of pairwise distances
of all spatial units it can take a significant amount of computation time. The
parameters approx
and nn
can be set to speed up the calculation
by approximation. The approximation can be achieved by using the Nyström
low-rank approximation method or by limiting the calculation of the paraview
to a number of nearest neighbors around each spatial unit.
If the value of approx
is between 0 and 1 it will be interpreted as
fraction of the number of spatial units. Discrete values above 1 will be
interpreted as the size of the approximation block. The number of nearest
neighbors nn
around each spatial unit are determined using a fast
nearest neighbor search.
If both approx
and nn
have non-null values, nn
has priority and an approximation based on fast nearest neighbor
search will be used to generate the paraview.
A mistyR view composition with added paraview with parameter l
.
create_initial_view()
for
starting a view composition with an intraview only.
Other view composition functions:
add_juxtaview()
,
add_views()
,
create_initial_view()
,
create_view()
,
remove_views()
# Create a view composition of an intraview and a paraview with radius 10. library(dplyr) # get the expression data data("synthetic") expr <- synthetic[[1]] %>% select(-c(row, col, type)) # get the coordinates for each cell pos <- synthetic[[1]] %>% select(row, col) # compose misty.views <- create_initial_view(expr) %>% add_paraview(pos, l = 10) # preview str(misty.views[["paraview.10"]])