/
_pkgdown.yml
200 lines (197 loc) · 5.51 KB
/
_pkgdown.yml
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destination: docs
reference:
- title: "GatingHierarchy and GatingSet classes"
desc: >
Classes for managing compensation, transformation,
and gating of cytometry data (FCS files) and methods for creating them
contents:
- GatingHierarchy-class
- GatingSet-class
- GatingSet-methods
- GatingSetList-class
- brackets
- identifier-methods
- convert_legacy_gs
- title: "cytoframe and cytoset classes"
desc: >
Reference classes for efficiently managing the representation of data from
FCS files (analagous to flowFrame and flowSet classes from the flowCore package)
contents:
- cytoframe
- cytoset
- convert
- load_cytoframe_from_fcs
- load_cytoframe_from_h5
- cf_get_h5_file_path
- cf_write_h5
- load_cytoset_from_fcs
- save_cytoset
- cs_add_cytoframe
- cs_set_cytoframe
- cs_get_h5_file_path
- load_meta
- lock
- cf_append_cols
- cytoframe-labels
- cf_keyword_insert
- title: "Examining the hierarchical gating tree"
desc: >
Functions for examining the subpopulations
resulting from applying gates to the data
contents:
- plot
- gs_plot_diff_tree
- gs_get_pop_paths
- gh_get_pop_paths
- gs_get_leaf_nodes
- gh_get_leaf_nodes
- gs_check_redundant_nodes
- gs_remove_redundant_nodes
- gh_get_cluster_labels
- gh_pop_get_cluster_name
- extract_cluster_pop_name_from_node
- gh_pop_get_full_path
- gs_pop_get_parent
- gs_pop_get_children
- gh_pop_get_children
- gh_pop_get_descendants
- gh_pop_get_stats
- gh_pop_get_stats_tfilter
- gs_pop_get_stats
- gs_pop_get_stats_tfilter
- gh_pop_compare_stats
- gh_plot_pop_count_cv
- gs_plot_pop_count_cv
- gh_pop_get_count
- gs_pop_get_count_fast
- gs_pop_get_count_with_meta
- gh_pop_get_proportion
- title: "Accessing underyling data"
desc: >
Functions for accessing or altering the flowFrame or
flowSet objects underlying the gating analysis. These
can also be useful in preparing GatingSet objects for merging.
contents:
- gs_is_h5
- gs_cyto_data
- gs_pop_get_data
- gh_pop_get_data
- gh_get_compensations
- gs_get_compensation_internal
- gh_get_transformations
- compensate
- transform
- gs_clone
- length
- sampleNames
- markernames
- pData
- keyword
- title: "Perform gating analysis"
desc: >
Functions for accessing, altering, adding, and removing
gate definitions and their resulting subpopulations. These
can also be useful in preparing GatingSet objects for merging.
contents:
- gh_pop_is_hidden
- gh_pop_set_visibility
- gh_pop_set_xml_count
- gh_pop_is_gated
- gh_pop_is_negated
- gh_pop_is_bool_gate
- gs_pop_get_gate
- gh_pop_get_gate
- gs_pop_set_gate
- gh_pop_set_gate
- recompute
- gs_pop_set_name
- gh_pop_set_name
- transform_gate
- rotate_gate
- scale_gate
- shift_gate
- subset.GatingSet
- gh_pop_get_indices
- gh_pop_get_indices_mat
- gh_pop_set_indices
- gs_get_singlecell_expression
- gs_get_singlecell_expression_by_gate
- pop.MFI
- pop_add
- gs_pop_add
- gh_pop_remove
- gs_pop_remove
- gh_pop_move
- gh_copy_gate
- gh_apply_to_new_fcs
- standardize-GatingSet
- gs_update_channels
- gs_remove_redundant_channels
- gs_split_by_channels
- gs_split_by_tree
- merge_list_to_gs
- lapply,GatingSet-method
- rbind2,GatingSetList,missing-method
- title: "Helpers to generate transformations and filters"
desc: >
Functions for quickly constructing transformations or filters
or converting them to a form that can be applied to data in
a GatingHierachy or GatingSet
contents:
- flow_trans
- transformerList
- estimateLogicle.GatingHierarchy
- filter_to_list
- asinh_Gml2
- asinhtGml2_trans
- logicle_trans
- logicleGml2_trans
- logtGml2_trans
- flowjo_fasinh
- flowjo_fasinh_trans
- flowjo_log_trans
- flowjo_biexp
- flowjo_biexp_trans
- booleanFilter
- title: "Read/write GatingSet objects"
desc: >
Functions to read save GatingSet objects to disk
or read them in to an R session
contents:
- save_gs
- load_gs
- save_gslist
- load_gslist
- title: "Plotting functions"
desc: >
Methods for plotting the hierarchical gating tree and gates.
More dedicated plotting methods for GatingSet and GatingHierarchy
objects are provided by the ggcyto package,
contents:
- plot
- plotGate-methods-defunct
- prettyAxis
- title: "Miscellaneous helper functions"
desc: >
Functions whose role does not easily fit in to one
of the above categories
contents:
- get_log_level
- flowWorkspace.par.set
- compute_timestep
- fix_channel_slash
- flow_breaks
- swap_data_cols
- cleanup_temp
navbar:
title: flowWorkspace
right:
- icon: fas fa fa-github fa-lg
href: https://github.com/RGLab/flowWorkspace
articles:
- title: Introduction
contents:
- flowWorkspace-Introduction
- title: How to merge GatingSets
contents:
- HowToMergeGatingSet