Start here: create a basic view composition with an intraview

This function is the first one to be called when building a mistyR workflow, starting from view composition. The initial view describes the intraview of the sample.

Usage

create_initial_view(data, unique.id = NULL)

Arguments

data

A data.frame or a tibble containing expression information for all markers of interest (in named columns) for each spatial unit (in rows).

unique.id

A character vector. Identifier of the current sample. If not provided (unique.id = NULL) then an id is automatically generated by calculating the md5 hash of table.

Value

An initial mistyR view composition containing an intraview list item named described with abbreviation "intra" and data as provided in data and a misty.uniqueid list item containing the provided or automatically calculated unique.id. A cache folder for the sample will be automatically created in the working directory as a subfolder of .misty.temp/ with the same name as unique.id.

See also

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

Examples

# Create an intrinsic view from the first sample in the dataset synthetic.

library(dplyr)

# get the expression data
data("synthetic")
expr <- synthetic[[1]] %>% select(-c(row, col, type))

create_initial_view(expr)
#> $intraview
#> $intraview$abbrev
#> [1] "intra"
#> 
#> $intraview$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 0.0385 0.834 0.0157 0.236 1.18   1.18 2.55   0.382 0      0     0.588
#>  2 0.0327 0.119 0.0104 0.804 0.101  0    0.386  0     0      0.536 0    
#>  3 0.144  0.525 0.0140 0.334 0.434  1.67 1.61   0.472 0      0     0.379
#>  4 0.387  0.269 0.0367 0.502 0.241  0    0.913  0     0      0.418 0    
#>  5 0.163  0.195 0.118  0.232 0.203  0    0.162  0     0.160  0     0    
#>  6 0.203  0.178 0.0247 0.738 0.236  0    0.603  0     0      0.555 0    
#>  7 0.200  0.170 0.122  0.715 0.246  0    0.862  0     0      0.496 0    
#>  8 0.0642 0.162 0.0999 0.549 0.243  0    0.0636 0     0.0623 0     0    
#>  9 0.0331 0.229 0.0404 0.246 0.378  0    0.0328 0     0.0322 0     0    
#> 10 0.268  0.146 0.0186 0.944 0.232  0    0.490  0     0      0.583 0    
#> # ℹ 4,195 more rows
#> 
#> 
#> $misty.uniqueid
#> [1] "b98ad35f4e671871cba35f2155228612"
#>