Convert polarization score table to an Assay or Assay5

Usage

PolarizationScoresToAssay(object, ...)

# S3 method for data.frame
PolarizationScoresToAssay(object, values_from = c("morans_z", "morans_i"), ...)

# S3 method for MPXAssay
PolarizationScoresToAssay(object, values_from = c("morans_z", "morans_i"), ...)

# S3 method for CellGraphAssay
PolarizationScoresToAssay(object, values_from = c("morans_z", "morans_i"), ...)

# S3 method for CellGraphAssay5
PolarizationScoresToAssay(object, values_from = c("morans_z", "morans_i"), ...)

# S3 method for Seurat
PolarizationScoresToAssay(
  object,
  assay = NULL,
  new_assay = NULL,
  values_from = c("morans_z", "morans_i"),
  ...
)

Arguments

object: An object with polarization scores
...: Not yet implemented
values_from: What column to pick polarization scores from. Either "morans_i" or "morans_z"
assay: Name of the CellGraphAssay to pull polarization scores from
new_assay: Name of the Assay to store the polarization scores in

Behavior

Takes an object with polarization scores in long format and returns an object with polarization scores in a wide format. The polarization score table includes Moran's I and Z scores along with p-values for each marker and component.

The wide format is an array-like object with dimensions markers x components, where each cell is filled with a polarization score. Scores that are missing from the polarization score table are replaced with 0's.

Different outputs are returned depending on the input object type:

tibble/data.frame: returns a matrix with markers in rows and components in columns
CelGraphAssay: returns an Assay with markers in rows and components in columns
Seurat object: returns the Seurat object with a new Assay with markers in rows and components in columns

As many functions provided in Seurat works on Assay objects, it is sometimes convenient to make this conversion. For instance, if we want to compute a UMAP on the polarization scores with RunUMAP, we need the values to be formatted in an Assay. This also makes it possible to use various visualization functions such as VlnPlot or FeaturePlor to show the distribution of polarization scores.

Examples

library(pixelatorR)
library(SeuratObject)

# Load example data as a Seurat object
pxl_file <- system.file("extdata/five_cells",
  "five_cells.pxl",
  package = "pixelatorR"
)
pol_scores <- ReadMPX_polarization(pxl_file)
#> ℹ Loading item(s) from: /private/var/folders/gw/bdcqhnvs0m9gs_mq8n51jtbc0000gn/T/RtmpMJapOH/temp_libpatha88241f348a/pixelatorR/extdata/five_cells/five_cells.pxl
#> →   Loading polarization data
#> ✔ Returning a 'tbl_df' object

# PolarizationScoresToAssay returns a matrix for a tbl_df
pol_scores_mat <- PolarizationScoresToAssay(pol_scores)
pol_scores_mat[1:4, 1:5]
#>       RCVCMP0000217 RCVCMP0000118 RCVCMP0000655 RCVCMP0000487 RCVCMP0000263
#> ACTB     -0.1335030    0.00000000    -0.2925391   -0.17816347    -0.1473378
#> B2M      -0.6759472    4.55113840     1.6401548   -3.14104176    -8.7973738
#> CD102    -0.8262732    0.03074864     0.3773469    0.03870055    -0.4982260
#> CD11a     0.1816744    0.07436839     0.8086415    0.30911581    -1.8365308

# Create a Seurat object
seur <- ReadMPX_Seurat(pxl_file)
#> ✔ Created a 'Seurat' object with 5 cells and 80 targeted surface proteins

# Fetch CellGraphAssay and create new polarization
# scores Assay
cg_assay <- seur[["mpxCells"]]
class(cg_assay)
#> [1] "CellGraphAssay"
#> attr(,"package")
#> [1] "pixelatorR"
pol_assay <- PolarizationScoresToAssay(cg_assay)
class(pol_assay)
#> [1] "Assay"
#> attr(,"package")
#> [1] "SeuratObject"

# Convert polarization scores within a Seurat object
seur <- PolarizationScoresToAssay(seur)

# After conversion, we now have a new assay called "polarization"
seur[["polarization"]]
#> Assay data with 80 features for 5 cells
#> First 10 features:
#>  ACTB, B2M, CD102, CD11a, CD11b, CD11c, CD127, CD137, CD14, CD150 

# Switch default assay to polarization
DefaultAssay(seur) <- "polarization"

# Visualize polarization scores with Seurat
# VlnPlot(seur, features = "CD19") +
#   labs(y = "Polarization score")

Convert polarization score table to an Assay or Assay5

Usage

Arguments

Behavior

See also

Examples