Package 'chevreulShiny'

Update a database of chevreulShiny projects

Description

Append projects to database

Usage

append_to_project_db(
  new_project_path,
  cache_location = "~/.cache/chevreul",
  sqlite_db = "single-cell-projects.db",
  verbose = TRUE
)

Arguments

new_project_path	new project path
cache_location	Path to cache "~/.cache/chevreul"
sqlite_db	sqlite db
verbose	print messages

Value

a sqlite database with SingleCellExperiment objects

---

Cyclone cell cycle pairs by symbol

Description

cell cycle genes with paired expression represented by HGNC symbol

Usage

cc.genes.cyclone

Format

a list of dataframes with G1, G2, and S gene expression

G1

G1 gene symbols

G2

G2 gene symbols

S

S gene symbols

...

Source

cyclone

---

Create a shiny app for a project on disk

Description

Create a shiny app for a project on disk

Usage

chevreulApp(
  preset_project,
  appTitle = "chevreul",
  organism_type = "human",
  futureMb = 13000,
  db_name = "single-cell-projects.db"
)

Arguments

preset_project	A preloaded project to start the app with
appTitle	A title of the App
organism_type	human or mouse
futureMb	amount of Mb allocated to future package
db_name	sqlite database with list of saved SingleCellExperiment objects

Value

a shiny app

---

Create a Table of single Cell Projects

Description

Uses a list of projects to create a matrix of single cell projects

Usage

create_proj_matrix(proj_list)

Arguments

proj_list

List of projects

Value

a tibble of single cell projects

---

Create a database of chevreulShiny projects

Description

Create a database containing chevreulShiny projects

Usage

create_project_db(
  cache_location = "~/.cache/chevreul",
  sqlite_db = "single-cell-projects.db",
  verbose = TRUE
)

Arguments

cache_location	Path to cache "~/.cache/chevreul"
sqlite_db	Database to be created
verbose	print messages

Value

a sqlite database with SingleCellExperiment objects

---

Ensembl version used for build

Description

Ensembl version used for build

Usage

ensembl_version

Format

An object of class character of length 1.

Source

http://www.ensembl.org/

Examples

# ensembl_version

---

Get Transcripts in object

Description

Get transcript ids in objects for one or more gene of interest

Usage

get_transcripts_from_sce(object, gene)

Arguments

object	A SingleCellExperiment object
gene	Gene of interest

Value

transcripts constituting a gene of interest in a SingleCellExperiment object

---

Human annotation data

Description

Human (Homo sapiens) annotations based on genome assembly GRCH38 from Ensembl.

Usage

grch38

Format

An object of class tbl_df (inherits from tbl, data.frame) with 76062 rows and 9 columns.

Details

Variables:

• ensgene

• entrez

• symbol

• chr

• start

• end

• strand

• biotype

• description

Source

http://ensembl.org/homo_sapiens

Examples

data("grch38")
head(grch38)

---

Human transcripts to genes

Description

Lookup table for converting Human (Homo sapiens) Ensembl transcript IDs to gene IDs based on genome assembly GRCH38 from Ensembl.

Usage

grch38_tx2gene

Format

An object of class tbl_df (inherits from tbl, data.frame) with 277081 rows and 2 columns.

Details

Variables:

• enstxp

• ensgene

Source

http://ensembl.org/homo_sapiens

Examples

data(grch38_tx2gene)
head(grch38_tx2gene)

---

Gene Homologs Between Human and Mouse

Description

Homologs drawn from Biomart

Usage

human_to_mouse_homologs

Format

A data frame with 23188 rows and 2 columns

HGNC.symbol

human gene symbols

MGI.symbol

mouse gene symbols

...

Source

bioMart

---

Collate list of variables to be plotted

Description

Collate list of variables to be plotted

Usage

list_plot_types(object)

Arguments

object

a SingleCellExperiment object

Value

plot_types a list of category_vars or continuous_vars

Examples

data(small_example_dataset)
list_plot_types(small_example_dataset)

---

Load SingleCellExperiment Files from a single project path

Description

Load SingleCellExperiment Files from a single project path

Usage

load_alabaster_from_proj(proj_dir, ...)

Arguments

proj_dir	project directory
...	extra args passed to load_alabaster_path

Value

a SingleCellExperiment object

---

Read in Gene and Transcript SingleCellExperiment Objects

Description

Read in Gene and Transcript SingleCellExperiment Objects

Usage

load_alabaster_path(proj_dir = getwd(), prefix = "unfiltered")

Arguments

proj_dir	path to project directory
prefix	default "unfiltered"

Value

a SingleCellExperiment object

---

Load Bigwigs

Description

Load a tibble of bigwig file paths by cell id

Usage

load_bigwigs(object, bigwig_db = "~/.cache/chevreul/bw-files.db")

Arguments

object	A object
bigwig_db	Sqlite database of bigwig files

Value

a vector of bigwigs file paths

---

Make Bigwig Database

Description

Make Bigwig Database

Usage

make_bigwig_db(
  new_project = NULL,
  cache_location = "~/.cache/chevreul/",
  sqlite_db = "bw-files.db"
)

Arguments

new_project	Project directory
cache_location	Path to cache "~/.cache/chevreul"
sqlite_db	sqlite db containing bw files

Value

a sqlite database of bigwig files for cells in a SingleCellExperiment object

---

Clean Vector of chevreulShiny Names

Description

Cleans names of objects provided in a vector form

Usage

make_chevreul_clean_names(myvec)

Arguments

myvec

A vector of object names

Value

a clean vector of object names

Examples

data(small_example_dataset)
make_chevreul_clean_names(colnames(
get_colData(small_example_dataset)))

---

Retrieve Metadata from Batch

Description

Retrieve Metadata from Batch

Usage

metadata_from_batch(
  batch,
  projects_dir = "/dataVolume/storage/single_cell_projects",
  db_path = "single-cell-projects.db"
)

Arguments

batch	batch
projects_dir	path to project dir
db_path	path to .db file

Value

a tibble with cell level metadata from a SingleCellExperiment object

---

Create a minimal chevreulShiny app using SingleCellExperiment input

Description

Create a minimal chevreulShiny app using SingleCellExperiment input

Usage

minimalChevreulApp(
  single_cell_sce = NULL,
  appTitle = NULL,
  organism_type = "human",
  futureMb = 13000,
  db_name = "single-cell-projects.db"
)

Arguments

single_cell_sce	a singlecell object
appTitle	a title for the app
organism_type	human or mouse
futureMb	the megabytes available for the future package
db_name	a database of bigwig files

Value

a minimal chevreulShiny app

Examples

if (interactive() ) {
  data("tiny_sce")
  minimalChevreulApp(tiny_sce)
}

---

Plot BigWig Coverage for Genes of Interest by a Given Variable

Description

Plot BigWig coverage for genes of interest colored by a given variable

Usage

plot_gene_coverage_by_var(
  genes_of_interest = "NRL",
  cell_metadata,
  bigwig_tbl,
  group_by = "batch",
  values_of_interest = NULL,
  organism = c("human", "mouse"),
  edb = NULL,
  heights = c(3, 1),
  scale_y = "log10",
  reverse_x = FALSE,
  start = NULL,
  end = NULL,
  summarize_transcripts = FALSE,
  ...
)

Arguments

genes_of_interest	Gene of interest
cell_metadata	a dataframe with cell metadata from object
bigwig_tbl	a tibble with colnames "name", "bigWig", and "sample_id" matching the filename, absolute path, and sample name of each cell in the cell_metadata
group_by	Variable to color by
values_of_interest	values of interest
organism	human (default) or mouse
edb	ensembldb object
heights	The heights of each row in the grid of plot
scale_y	whether to scale coverage
reverse_x	whether to reverse x axis
start	start coordinates
end	end coordinates
summarize_transcripts	whether to summarize transcript counts
...	extra arguments passed to plotCoverageFromEnsembldb

Value

a ggplot with coverage faceted by group_by

---

Plotly settings

Description

Change settings of a plotly plot

Usage

plotly_settings(plotly_plot, width = 600, height = 700)

Arguments

plotly_plot	A plotly plot
width	Default set to '600'
height	Default set to '700'

Value

a plotly plot with settings changed

---

Read a database of chevreulShiny projects

Description

Reads database of chevreulShiny projects to a data frame

Usage

read_project_db(
  cache_location = "~/.cache/chevreul",
  sqlite_db = "single-cell-projects.db",
  verbose = TRUE
)

Arguments

cache_location	Path to cache "~/.cache/chevreul"
sqlite_db	sqlite db
verbose	print messages

Value

a tibble with SingleCellExperiment objects

---

Save object to /output/sce/_sce.rds

Description

Save object to /output/sce/_sce.rds

Usage

save_sce(object, prefix = "unfiltered", proj_dir = getwd())

Arguments

object	a SingleCellExperiment object
prefix	a prefix for saving
proj_dir	path to a project directory

Value

a path to an rds file containing a SingleCellExperiment object

---

Small example SingleCellExperiment

Description

created with scuttle::mockSCE

Usage

small_example_dataset

Format

An SCE with 200 cells and 1000 genes

Source

scuttle::mockSCE

---

Subset by new colData

Description

Subset the object using new colData

Usage

subset_by_colData(colData_path, object)

Arguments

colData_path	Path to new colData
object	A object

Value

a SingleCellExperiment object

---

Tiny example SingleCellExperiment

Description

subset to only NRL from chevreuldata::human_gene_transcript_sce()

Usage

tiny_sce

Format

An SCE with only expression of NRL gene and NRL transripts

Source

chevreuldata::human_gene_transcript_sce()

---

Unite metadata

Description

Unite metadata

Usage

unite_metadata(object, group_bys)

Arguments

object	A SingleCellExperiment object
group_bys	A feature or variable to combine

Value

a SingleCellExperiment object with Idents formed from concatenation of group_bys

Examples

data(small_example_dataset)
unite_metadata(small_example_dataset, "Mutation_Status")

---

Update a database of chevreulShiny projects

Description

Add new/update existing projects to the database by recursing fully

Usage

update_project_db(
  projects_dir = NULL,
  cache_location = "~/.cache/chevreul",
  sqlite_db = "single-cell-projects.db",
  verbose = TRUE
)

Arguments

projects_dir	The project directory to be updated
cache_location	Path to cache "~/.cache/chevreul"
sqlite_db	sqlite db
verbose	print messages

Value

a sqlite database with SingleCellExperiment objects

---