Package 'phenomenalist'

Title: Analysis Toolkit for PhenoCycler (CODEX) Data in R
Description: A collection of tools for cleaning, clustering, and plotting PhenoCycler (CODEX) data.
Authors: Igor Dolgalev [aut, cre]
Maintainer: Igor Dolgalev <[email protected]>
License: MIT + file LICENSE
Version: 0.0.0.9003
Built: 2025-03-23 06:26:49 UTC
Source: https://github.com/igordot/phenomenalist

Help Index

Clean up data frame column names

Description

Clean up data frame column names

Usage

clean_col_names(x)

Arguments

x

A data frame.

Value

A data frame.

Perform clustering

Description

Cluster similar cells based on their expression profiles.

Usage

cluster(
  x,
  method = c("leiden"),
  resolution = 1,
  n_neighbors = 50,
  out_dir = NULL
)

Arguments

x

A SpatialExperiment object.
method

Clustering method (only leiden is implemented currently).
resolution

Value of the parameter controlling the coarseness of the clusters (higher resolution yields more clusters).
n_neighbors

The maximum number of nearest neighbors to compute.
out_dir

Name of the output analysis directory. If specified, the object and the corresponding plots will be saved there.

Value

A SpatialExperiment object.

Create a SpatialExperiment object

Description

Create a SpatialExperiment object (used in the same manner as SingleCellExperiment) that will store all of the project data.

Usage

create_object(
  x,
  expression_cols = NULL,
  metadata_cols = NULL,
  skip_cols = NULL,
  clean_names = TRUE,
  transformation = NULL,
  out_dir = NULL
)

Arguments

x

A data frame or a path to a file (can be gzipped).
expression_cols

Column names of markers/antibody expression as a vector or a grep pattern. Auto-detected if not specified.
metadata_cols

Column names of cell metadata (not markers/antibodies) as a vector or a grep pattern. Auto-detected if not specified.
skip_cols

Column names to ignore (such as bad antibodies) as a vector or a grep pattern.
clean_names

A logical scalar. Clean the data frame column names to remove problematic characters and make them unique.
transformation

A character string indicating which transformation method should be used. See transform().
out_dir

Name of the output analysis directory. If specified, the object and the corresponding plots will be saved there.

Value

A SpatialExperiment object.

Examples

tonsil_csv <- system.file("extdata", "tonsil-akoya-2018-500.csv", package = "phenomenalist")
tonsil_spe <- create_object(tonsil_csv, skip_cols = "DAPI|Blank", transformation = "z")

Detect marker/antibody column names

Description

The input is generally a table of both expression values and various metadata columns. This function attempts to determine which of the columns contain expression values.

Usage

detect_exprs_cols(x)

Arguments

x

A data frame.

Value

A vector of column names.

Plot expression distribution

Description

Plot distribution of expression intensities, split by marker.

Usage

plot_distribution(x, assay = "exprs", out_dir = NULL)

Arguments

x

A SpatialExperiment object.
assay

A character string indicating which values should be used.
out_dir

Name of the output analysis directory. If specified, the plots will be saved there.

Value

.

Plot dimensionality reduction

Description

Plot cell-level reduced dimension results stored in a SpatialExperiment object.

Usage

plot_dr(
  x,
  dr,
  color_by,
  assay = "logcounts",
  smooth = FALSE,
  range = c(0.01, 0.99),
  out_dir = NULL
)

Arguments

x

A SpatialExperiment object.
dr

.
color_by

Column metadata field(s) or feature(s) to color by.
assay

A character string indicating which expression values should be used.
smooth

A logical scalar. Smooth values. Helps to visualize expression patterns in a plot with many overlapping points.
range

A vector of 2 values indicating the minimum and maximum percentiles for the color range. Helps to visualize expression patterns when extreme outliers are present. For example, c(0, 0.99) will not expand the color scale above 99th percentile.
out_dir

Name of the output analysis directory. If specified, the plots will be saved there.

Value

.

Generate a heatmap

Description

Generate a heatmap

Usage

plot_heatmap(x, group_by, assay = "logcounts", out_dir = NULL)

Arguments

x

A SpatialExperiment object.
group_by

Column metadata field(s) to group by.
assay

A character string indicating which expression values should be used.
out_dir

Name of the output analysis directory. If specified, the plots will be saved there.

Value

A Heatmap object.

Generate a generic scatter plot

Description

Create a scatter plot to display the relationship between two continuous variables. This is essentially a wrapper for ggplot2::geom_point().

Usage

plot_scatter(
  data,
  x,
  y,
  color_by,
  smooth = FALSE,
  range = c(0.01, 0.99),
  title = "",
  aspect_ratio = 1
)

Arguments

data

A data frame.
x

.
y

.
color_by

Column metadata field(s) or feature(s) to color by.
smooth

A logical scalar. Smooth values. Helps to visualize expression patterns in a plot with many overlapping points.
range

A vector of 2 values indicating the minimum and maximum percentiles for the color range. Helps to visualize expression patterns when extreme outliers are present. For example, c(0, 0.99) will not expand the color scale above 99th percentile.
title

Plot title.
aspect_ratio

Aspect ratio of the panel.

Value

A ggplot object.

Plot cells on their spatial coordinates

Description

Plot cell-level physical coordinates stored in a SpatialExperiment object.

Usage

plot_spatial(
  x,
  color_by,
  assay = "logcounts",
  smooth = FALSE,
  range = c(0.01, 0.99),
  out_dir = NULL
)

Arguments

x

A SpatialExperiment object.
color_by

Column metadata field(s) or feature(s) to color by.
assay

A character string indicating which expression values should be used.
smooth

A logical scalar. Smooth values. Helps to visualize expression patterns in a plot with many overlapping points.
range

A vector of 2 values indicating the minimum and maximum percentiles for the color range. Helps to visualize expression patterns when extreme outliers are present. For example, c(0, 0.99) will not expand the color scale above 99th percentile.
out_dir

Name of the output analysis directory. If specified, the plots will be saved there.

Value

.

Run UMAP dimensionality reduction

Description

Run UMAP dimensionality reduction

Usage

run_umap(
  x,
  assay = "exprs",
  n_neighbors = 50,
  min_dist = 0.01,
  n_threads = NULL,
  out_dir = NULL
)

Arguments

x

A SpatialExperiment object.
assay

.
n_neighbors

The size of local neighborhood (in terms of number of neighboring sample points) used for manifold approximation. Larger values result in more global views of the manifold, while smaller values result in more local data being preserved. In general values should be in the range 2 to 100.
min_dist

The effective minimum distance between embedded points. Smaller values will result in a more clustered/clumped embedding where nearby points on the manifold are drawn closer together, while larger values will result on a more even dispersal of points. The value should be set relative to the spread value, which determines the scale at which embedded points will be spread out.
n_threads

Number of threads to use (except during stochastic gradient descent). Default is half the number of concurrent threads supported by the system. For nearest neighbor search, only applies if nn_method = "annoy". If n_threads > 1, then the Annoy index will be temporarily written to disk in the location determined by tempfile.
out_dir

Name of the output analysis directory. If specified, the object will be saved there.

Value

A SpatialExperiment object.

Transform/normalize expression data

Description

Transform/normalize expression data. The options are currently:

  • log: log10 + 1

  • z: Z normalization of each marker (recommended by Hickey et al.)

Usage

transform(x, method = c("log", "z"), out_dir = NULL)

Arguments

x

A SpatialExperiment object.
method

A character string indicating which transformation method should be used.
out_dir

Name of the output directory. If specified, the density plots will be saved there.

Value

A SpatialExperiment object with transformed values in the exprs assay.