Print, summarise and measure a cellspec object

print() shows a compact overview that fits in 80 columns: cells, images, samples, features by kind, markers, pixel size, specification version and the adapter that produced the object. summary() returns one row per image. dim() returns the number of cells and features.

Usage

# S3 method for class 'cellspec'
print(x, ...)

# S3 method for class 'cellspec'
summary(object, ...)

# S3 method for class 'cellspec_summary'
print(x, ...)

# S3 method for class 'cellspec'
dim(x)

Arguments

x, object

A cellspec object (or, for the summary print method, a cellspec_summary).

...

Unused; for compatibility with the generics.

Value

• print() returns x invisibly.

• summary() returns a data frame of class cellspec_summary with one row per image and the columns image_id, sample_id (character), n_cells, n_markers, n_features (integer; markers and features with at least one non-missing value in that image), pixel_size, x_min, x_max, y_min, y_max (double, micrometres) and na_fraction (double, fraction of missing measurement values in that image).

• dim() returns an integer vector c(cells, features).

See also

Other methods: [.cellspec(), as.data.frame.cellspec(), plot.cellspec()

Examples

x <- cs_example()
x
#> <cellspec> spec 1.0.0
#>   cells     80 in 2 images (2 samples)
#>   features  19: 16 intensity, 2 shape, 1 other
#>   markers   4: DAPI, CD3e, Pan-Cytokeratin, FOXP3
#>   pixel     0.5 um/px
#>   adjacency none
#>   source    simulate 1.0.0 (cellspecR simulator 1.1.0)
summary(x)
#> <cellspec summary> 2 images, 80 cells
#>  image_id sample_id n_cells n_markers n_features pixel_size  x_min  x_max
#>      img1        s1      40         4         19        0.5 22.498 504.86
#>      img2        s2      40         4         19        0.5 17.146 494.75
#>   y_min  y_max na_fraction
#>  20.589 508.74           0
#>   1.152 500.00           0
dim(x)
#> [1] 80 19