Summarize proximity scores

Computes the median or mean proximity score for each protein pair across all group combinations defined by group_vars. This is typically useful when profiling a population of interest, where the goal is to compute representative proximity scores for each protein pair within that population.

The proximity table typically contains a small fraction of the possible protein pairs for each cell. These missing pairs typically have UMI counts below the detection threshold and their proximity scores can therefore be imputed as 0 (0 observed join counts and 0 expected join counts => no deviation from the expected value). SummarizeProximityScores pads the proximity score vectors with 0s for the missing pairs to ensure that the summary statistics are computed for the entire population. This behavior can be turned off by setting include_missing_obs = FALSE.

Usage

SummarizeProximityScores(object, ...)

# S3 method for class 'tbl_lazy'
SummarizeProximityScores(
  object,
  proximity_metric = c("log2_ratio", "join_count_z"),
  group_vars = NULL,
  include_missing_obs = TRUE,
  summary_stat = c("mean", "median"),
  detailed = FALSE,
  ...
)

# S3 method for class 'data.frame'
SummarizeProximityScores(
  object,
  proximity_metric = "log2_ratio",
  group_vars = NULL,
  include_missing_obs = TRUE,
  summary_stat = c("mean", "median"),
  detailed = FALSE,
  ...
)

Arguments

object

A tbl_df or tbl_lazy object with proximity scores.

...

Additional arguments. Currently not used.

proximity_metric

The proximity metric to use. One of "log2_ratio" or "join_count_z".

group_vars

A character vector with the names of the variables to use for grouping This is typically used is you want to summarize the proximity scores for multiple cell types and/or conditions.

include_missing_obs

Logical indicating whether to include missing observations as 0 when computing the summary statistics.

summary_stat

One of "mean" or "median"

detailed

Logical indicating whether to return lists which can be used to compute custom summary statistics. See examples for details

Value

A tbl_df with summary statistics

Examples

library(pixelatorR)
library(dplyr)

pxl_file <- minimal_pna_pxl_file()
se <- ReadPNA_Seurat(pxl_file)
proximity_table <- ProximityScores(se)

# Default method uses mean
SummarizeProximityScores(proximity_table) %>% head()
#> # A tibble: 6 × 7
#>   marker_1 marker_2 n_cells_detected n_cells n_cells_missing pct_detected
#>   <chr>    <chr>               <int>   <int>           <int>        <dbl>
#> 1 CD56     TCRgd                   3       5               2          0.6
#> 2 CD366    CD41                    5       5               0          1  
#> 3 CD366    CD49D                   5       5               0          1  
#> 4 CD366    CD81                    5       5               0          1  
#> 5 CD366    CD369                   4       5               1          0.8
#> 6 CD366    CD64                    5       5               0          1  
#> # ℹ 1 more variable: mean_log2_ratio <dbl>

# Switch to median
SummarizeProximityScores(proximity_table, summary_stat = "median") %>% head()
#> # A tibble: 6 × 7
#>   marker_1 marker_2 n_cells_detected n_cells n_cells_missing pct_detected
#>   <chr>    <chr>               <int>   <int>           <int>        <dbl>
#> 1 CD56     CD56                    4       5               1          0.8
#> 2 CD56     CD85j                   4       5               1          0.8
#> 3 CD56     CD70                    2       5               3          0.4
#> 4 CD366    CD52                    5       5               0          1  
#> 5 CD366    CD89                    5       5               0          1  
#> 6 CD366    CD73                    5       5               0          1  
#> # ℹ 1 more variable: median_log2_ratio <dbl>

# Ignore missing values
SummarizeProximityScores(proximity_table, include_missing_obs = FALSE) %>% head()
#> # A tibble: 6 × 7
#>   marker_1 marker_2 n_cells_detected n_cells n_cells_missing pct_detected
#>   <chr>    <chr>               <int>   <int>           <int>        <dbl>
#> 1 CD56     HLA-ABC                 4       5               1          0.8
#> 2 CD56     IgD                     4       5               1          0.8
#> 3 CD56     CD9                     4       5               1          0.8
#> 4 CD366    CD37                    5       5               0          1  
#> 5 CD366    IgM                     5       5               0          1  
#> 6 CD366    TCRva7.2                5       5               0          1  
#> # ℹ 1 more variable: mean_log2_ratio <dbl>

# Return lists which can be used to compute custom summary statistics
SummarizeProximityScores(proximity_table, detailed = TRUE) %>%
  # It's important to do rowwise computations
  rowwise() %>%
  mutate(
    sd = sd(unlist(log2_ratio_list)),
    iqr = IQR(unlist(log2_ratio_list)),
    mad = mad(unlist(log2_ratio_list)),
    q90 = quantile(unlist(log2_ratio_list), 0.9)
  ) %>%
  select(marker_1, marker_2, sd, iqr, mad, q90) %>%
  ungroup()
#> # A tibble: 12,561 × 6
#>    marker_1 marker_2    sd   iqr   mad   q90
#>    <chr>    <chr>    <dbl> <dbl> <dbl> <dbl>
#>  1 CD56     Siglec-9 0     0     0     0    
#>  2 CD56     CD79a    0     0     0     0    
#>  3 CD56     GPR56    0     0     0     0    
#>  4 CD366    CD71     0     0     0     0    
#>  5 CD366    CD44     0.734 0.203 0.297 0.145
#>  6 CD366    CD59     0.416 0.575 0.545 0    
#>  7 CD366    CD48     0.739 0.876 0     0    
#>  8 CD366    CX3CR1   0.447 0     0     0.600
#>  9 CD52     mIgG1    0.560 0.485 0     0    
#> 10 CD37     CD52     1.07  0.337 0.412 0.624
#> # ℹ 12,551 more rows