Create a custom view

Create a custom view from a data.frame or a tibble.

Usage

create_view(name, data, abbrev = name)

Arguments

name

Name of the view. A character vector.

data

A data.frame or a tibble with named variables in columns and rows for each spatial unit ordered as in the intraview.

abbrev

Abbreviated name. A character vector.

Value

A new mistyR view. A list with a single named item described by the provided abbreviation and data containing the provided

data.

Details

Creating a custom view does not add it to the current view composition.

See also

add_views() for adding created views to a view composition.

Other view composition functions: add_juxtaview(), add_paraview(), add_views(), create_initial_view(), remove_views()

Examples

# Create a view from the mean expression of the 10 nearest neighbors of
# each cell.

library(dplyr)
library(purrr)
library(distances)

# 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)

# find the 10 nearest neighbors
neighbors <- nearest_neighbor_search(distances(as.matrix(pos)), k = 11)[-1, ]

# calculate the mean expression of the nearest neighbors for all markers
# for each cell in expr
nnexpr <- seq_len(nrow(expr)) %>%
  map_dfr(~ expr %>%
    slice(neighbors[, .x]) %>%
    colMeans())

create_view("nearest", nnexpr, "nn")
#> $nearest
#> $nearest$abbrev
#> [1] "nn"
#> 
#> $nearest$data
#> # A tibble: 4,205 × 11
#>      ECM  ligA   ligB  ligC  ligD protE protF  prodA  prodB  prodC  prodD
#>    <dbl> <dbl>  <dbl> <dbl> <dbl> <dbl> <dbl>  <dbl>  <dbl>  <dbl>  <dbl>
#>  1 0.169 0.449 0.0349 0.242 0.619 0.337 1.07  0.120  0.0138 0.146  0.165 
#>  2 0.346 0.223 0.0303 0.478 0.191 0.676 0.549 0.0969 0.0140 0.190  0.0766
#>  3 0.219 0.242 0.0375 0.456 0.218 0.304 0.495 0.0496 0.0288 0.236  0.0387
#>  4 0.238 0.312 0.0433 0.311 0.303 0.607 0.651 0.132  0.0288 0.0954 0.122 
#>  5 0.313 0.341 0.0480 0.269 0.357 0.688 0.835 0.166  0.0297 0.0837 0.173 
#>  6 0.527 0.257 0.0668 0.369 0.346 0.743 0.616 0.0722 0.0184 0.135  0.0964
#>  7 0.278 0.241 0.0952 0.480 0.347 0.399 0.501 0.0413 0.0632 0.160  0.0604
#>  8 0.266 0.260 0.0912 0.444 0.385 0.537 0.624 0.0738 0.0463 0.154  0.117 
#>  9 0.356 0.210 0.0811 0.522 0.311 0.564 0.565 0.0696 0.0415 0.208  0.106 
#> 10 0.625 0.152 0.0923 0.612 0.229 0.863 0.458 0.0350 0.0823 0.230  0.0576
#> # ℹ 4,195 more rows
#> 
#>