Azimuth-package: Azimuth: A Shiny App Demonstrating a Query-Reference Mapping...
In satijalab/azimuth: A Shiny App Demonstrating a Query-Reference Mapping Algorithm for Single-Cell Data
Azimuth-package R Documentation
Azimuth: A Shiny App Demonstrating a Query-Reference Mapping Algorithm for Single-Cell Data
Description
Azimuth uses an annotated reference dataset to automate the processing, analysis, and interpretation of a new single-cell RNA-seq or ATAC-seq experiment. Azimuth leverages a 'reference-based mapping' pipeline that inputs a counts matrix and performs normalization, visualization, cell annotation, and differential expression (biomarker discovery).
Package options
Azimuth uses the following options to control the behavior of the app.
Users can provide these as named arguments to AzimuthApp
through dots (...), specify these in the config file, or configure these with
options.
App options
The following options control app behavior
Azimuth.app.default_adt-
ADT to select by default in feature/violin plot
Azimuth.app.default_gene-
Gene to select by default in feature/violin plot
Azimuth.app.default_metadata-
Default metadata transferred from reference.
Azimuth.app.demodataset-
Path to data file (in any Azimuth-supported format) to automatically load
when the user clicks a button. The button is only available in the UI
if this option is set
Azimuth.app.googlesheet-
Google Sheet identifier (appropriate for use with
googlesheets4:gs4_get) to write log
records. Logging is only enabled if this and other google* options
are set
Azimuth.app.googletoken-
Path to directory containing Google Authentication token file.
Logging is only enabled if this and other google* options are set
Azimuth.app.googletokenemail-
Email address corresponding to the Google Authentication token file.
Logging is only enabled if this and other google* options are set
Azimuth.app.max_cells-
Maximum number of cells allowed to upload
Azimuth.app.metadata_notransfer-
Metadata to annotate in reference but not transfer to query
Azimuth.app.mito-
Regular expression pattern indicating mitochondrial features in query
object
Azimuth.app.plotseed-
Seed to shuffle colors for cell types
Azimuth.app.reference-
URL or directory path to reference dataset; see
LoadReference for more details
Azimuth.app.refuri-
URL for publicly available reference dataset, used in the downloadable
analysis script in case Azimuth.app.reference points to a directory
Azimuth.app.refdescriptor-
Provide (as a string) the html to render the reference description on the
welcome page
Azimuth.app.welcomebox-
Provide (as a string) the code to render the box on the welcome page
(quotes escaped). Example:
box(
h3(\"Header\"),
\"body text\",
a(\"link\", href=\"www.satijalab.org\", target=\"_blank\"),
width = 12
)
Azimuth.app.homologs-
URL or path to file containing the human/mouse homolog table.
Azimuth.app.metatableheatmap-
Display the meta.data table as a heatmap rather than in tabular form.
defaults to FALSE.
Azimuth.app.overlayedreference-
Display the mapped query on top of greyed out reference in the 'Cell
Plots' tab.
defaults to FALSE
Control options
These options control mapping and analysis behavior
Azimuth.map.ncells-
Minimum number of cells required to accept uploaded file
defaults to 100
Azimuth.map.ngenes-
Minimum number of genes in common with reference to accept uploaded file;
defaults to 250
Azimuth.map.nanchors-
Minimum number of anchors that must be found to complete mapping.
Defaults to 50
Azimuth.map.panchorscolors-
Configure the valuebox on the main page corresponding to the values for
failure, warning, success for fraction of unique query cells that
participate in anchor pairs. Failure corresponds to
[0:Azimuth.map.fracanchorscolors[1]), warning to
[Azimuth.map.fracanchorscolors[1]:Azimuth.map.fracanchorscolors[2]),
and success is >= Azimuth.map.fracanchorscolors[2].
Defaults to c(5, 15)
Azimuth.map.postmapqccolors-
Configure the valuebox on the main page corresponding to the values for
failure, warning, success for the post mapping cluster based QC metric.
Failure corresponds to [0:Azimuth.map.postmapqc[1]), warning to
[Azimuth.map.postmapqc[1]:Azimuth.map.postmapqc[2]),
and success is >= Azimuth.map.postmapqc[2].
Defaults to c(0.15, 0.25)
Azimuth.map.postmapqcds-
Set the amount of query random downsampling to perform before computing
the mapping QC metric.
Defaults to 5000
Azimuth.map.ntrees-
Annoy (approximate nearest neighbor) n.trees parameter
Defaults to 20
Azimuth.map.ndims-
Number of dimensions to use in FindTransferAnchors and TransferData
Defaults to 50
Azimuth.de.mincells-
Minimum number of cells per cluster for differential expression; defaults
to 15
Azimuth.de.digits-
Number of digits to round differential expression table to; defaults to
3
Azimuth.sct.ncells, Azimuth.sct.nfeats-
Number of cells and features to use for
SCTransform, respectively. Defaults to 2000
for each
External options
The following options are used by external dependencies that have an effect
on Azimuth's behavior. Refer to original package documentation for
more details
shiny.maxRequestSize-
User-configurable; used for controlling the maximum file size of uploaded
datasets. Defaults to 500 Mb
DT.options-
User-configurable; used for controlling biomarker table outputs.
Defaults to setting pageLength to 10
future.globals.maxSize-
Non-configurable; used for parallelization. Defaults to
Azimuth.app.max_cells * 320000
Author(s)
Maintainer: Paul Hoffman phoffman@nygenome.org (ORCID)
Authors:
Andrew Butler abutler@nygenome.org (ORCID)
Charlotte Darby cdarby@nygenome.org (ORCID)
Yuhan Hao yhao@nygenome.org (ORCID)
Austin Hartman ahartman@nygenome.org (ORCID)
Gesmira Molla gmolla@nygenome.org (ORCID)
Rahul Satija rsatija@nygenome.org (ORCID)
Other contributors:
Jaison Jain jjain@nygenome.org (ORCID) [contributor]
Satija Lab and Collaborators [funder]
See Also
Useful links:
satijalab/azimuth documentation built on Nov. 19, 2023, 8:34 a.m.
R Package Documentation
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| Azimuth-package | R Documentation |
Azimuth: A Shiny App Demonstrating a Query-Reference Mapping Algorithm for Single-Cell Data
Description
Azimuth uses an annotated reference dataset to automate the processing, analysis, and interpretation of a new single-cell RNA-seq or ATAC-seq experiment. Azimuth leverages a 'reference-based mapping' pipeline that inputs a counts matrix and performs normalization, visualization, cell annotation, and differential expression (biomarker discovery).
Package options
Azimuth uses the following options to control the behavior of the app.
Users can provide these as named arguments to AzimuthApp
through dots (...), specify these in the config file, or configure these with
options.
App options
The following options control app behavior
Azimuth.app.default_adt-
ADT to select by default in feature/violin plot
Azimuth.app.default_gene-
Gene to select by default in feature/violin plot
Azimuth.app.default_metadata-
Default metadata transferred from reference.
Azimuth.app.demodataset-
Path to data file (in any Azimuth-supported format) to automatically load when the user clicks a button. The button is only available in the UI if this option is set
Azimuth.app.googlesheet-
Google Sheet identifier (appropriate for use with
googlesheets4:gs4_get) to write log records. Logging is only enabled if this and othergoogle*options are set Azimuth.app.googletoken-
Path to directory containing Google Authentication token file. Logging is only enabled if this and other
google*options are set Azimuth.app.googletokenemail-
Email address corresponding to the Google Authentication token file. Logging is only enabled if this and other
google*options are set Azimuth.app.max_cells-
Maximum number of cells allowed to upload
Azimuth.app.metadata_notransfer-
Metadata to annotate in reference but not transfer to query
Azimuth.app.mito-
Regular expression pattern indicating mitochondrial features in query object
Azimuth.app.plotseed-
Seed to shuffle colors for cell types
Azimuth.app.reference-
URL or directory path to reference dataset; see
LoadReferencefor more details Azimuth.app.refuri-
URL for publicly available reference dataset, used in the downloadable analysis script in case
Azimuth.app.referencepoints to a directory Azimuth.app.refdescriptor-
Provide (as a string) the html to render the reference description on the welcome page
Azimuth.app.welcomebox-
Provide (as a string) the code to render the box on the welcome page (quotes escaped). Example:
box( h3(\"Header\"), \"body text\", a(\"link\", href=\"www.satijalab.org\", target=\"_blank\"), width = 12 )
Azimuth.app.homologs-
URL or path to file containing the human/mouse homolog table.
Azimuth.app.metatableheatmap-
Display the meta.data table as a heatmap rather than in tabular form. defaults to FALSE.
Azimuth.app.overlayedreference-
Display the mapped query on top of greyed out reference in the 'Cell Plots' tab. defaults to FALSE
Control options
These options control mapping and analysis behavior
Azimuth.map.ncells-
Minimum number of cells required to accept uploaded file defaults to
100 Azimuth.map.ngenes-
Minimum number of genes in common with reference to accept uploaded file; defaults to
250 Azimuth.map.nanchors-
Minimum number of anchors that must be found to complete mapping. Defaults to
50 Azimuth.map.panchorscolors-
Configure the valuebox on the main page corresponding to the values for failure, warning, success for fraction of unique query cells that participate in anchor pairs. Failure corresponds to [0:
Azimuth.map.fracanchorscolors[1]), warning to [Azimuth.map.fracanchorscolors[1]:Azimuth.map.fracanchorscolors[2]), and success is >=Azimuth.map.fracanchorscolors[2]. Defaults toc(5, 15) Azimuth.map.postmapqccolors-
Configure the valuebox on the main page corresponding to the values for failure, warning, success for the post mapping cluster based QC metric. Failure corresponds to [0:
Azimuth.map.postmapqc[1]), warning to [Azimuth.map.postmapqc[1]:Azimuth.map.postmapqc[2]), and success is >=Azimuth.map.postmapqc[2]. Defaults toc(0.15, 0.25) Azimuth.map.postmapqcds-
Set the amount of query random downsampling to perform before computing the mapping QC metric. Defaults to
5000 Azimuth.map.ntrees-
Annoy (approximate nearest neighbor) n.trees parameter Defaults to
20 Azimuth.map.ndims-
Number of dimensions to use in FindTransferAnchors and TransferData Defaults to
50 Azimuth.de.mincells-
Minimum number of cells per cluster for differential expression; defaults to
15 Azimuth.de.digits-
Number of digits to round differential expression table to; defaults to
3 Azimuth.sct.ncells,Azimuth.sct.nfeats-
Number of cells and features to use for
SCTransform, respectively. Defaults to2000for each
External options
The following options are used by external dependencies that have an effect on Azimuth's behavior. Refer to original package documentation for more details
shiny.maxRequestSize-
User-configurable; used for controlling the maximum file size of uploaded datasets. Defaults to 500 Mb
DT.options-
User-configurable; used for controlling biomarker table outputs. Defaults to setting
pageLengthto10 future.globals.maxSize-
Non-configurable; used for parallelization. Defaults to
Azimuth.app.max_cells * 320000
Author(s)
Maintainer: Paul Hoffman phoffman@nygenome.org (ORCID)
Authors:
Andrew Butler abutler@nygenome.org (ORCID)
Charlotte Darby cdarby@nygenome.org (ORCID)
Yuhan Hao yhao@nygenome.org (ORCID)
Austin Hartman ahartman@nygenome.org (ORCID)
Gesmira Molla gmolla@nygenome.org (ORCID)
Rahul Satija rsatija@nygenome.org (ORCID)
Other contributors:
Jaison Jain jjain@nygenome.org (ORCID) [contributor]
Satija Lab and Collaborators [funder]
See Also
Useful links:
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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