Package: flowGraph 1.21.0

Alice Yue

flowGraph: Identifying differential cell populations in flow cytometry data accounting for marker frequency

Identifies maximal differential cell populations in flow cytometry data taking into account dependencies between cell populations; flowGraph calculates and plots SpecEnr abundance scores given cell population cell counts.

Authors:Alice Yue [aut, cre]

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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
flowGraph/json (API)

# Install 'flowGraph' in R:

install.packages('flowGraph', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/aya49/flowgraph/issues

Datasets:

fg_data_fca - Fg_data_fca
fg_data_pos2 - Fg_data_pos2
fg_data_pos30 - Fg_data_pos30

On BioConductor:flowGraph-1.21.0(bioc 3.24)flowGraph-1.20.0(bioc 3.23)

flowcytometry statisticalmethod immunooncology software cellbasedassays visualization

4.04 score 1 stars 11 scripts 50 exports 75 dependencies

Last updated from:04c50272f4. Checks:1 WARNING, 7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	WARNING	178
linux-devel-x86_64	NOTE	359
source / vignettes	OK	244
linux-release-x86_64	NOTE	346
macos-release-arm64	NOTE	181
macos-oldrel-arm64	NOTE	174
windows-devel	NOTE	265
windows-release	NOTE	268
windows-oldrel	NOTE	257
wasm-release	OK	173

Exports:cell_type_layers fg_add_feature fg_add_summary fg_clear_features fg_clear_summary fg_extract_phenotypes fg_extract_raw fg_extract_samples fg_feat_edge_prop fg_feat_edge_specenr fg_feat_mean_class fg_feat_node_prop fg_feat_node_specenr fg_get_feature fg_get_feature_desc fg_get_feature_means fg_get_graph fg_get_markers fg_get_meta fg_get_summary fg_get_summary_desc fg_get_summary_index fg_get_summary_tables fg_gsub_ids fg_gsub_markers fg_load fg_merge fg_merge_samples fg_plot fg_plot_box fg_plot_pVSdiff fg_plot_qq fg_replace_meta fg_rm_feature fg_rm_summary fg_save fg_save_plots fg_set_layout fg_summary flowGraph flowGraphSubset flowGraphSubset_summary_adjust flowGraphSubset_summary_pars get_phen_list get_phen_meta ggdf plot_gr set_layout_graph show summary_table

Dependencies:base64enc bslib cachem cli codetools cpp11 data.table digest dplyr effsize evaluate farver fastmap fontawesome fontBitstreamVera fontLiberation fontquiver fs furrr future gdtools generics ggiraph ggplot2 ggrepel globals glue gridExtra gtable highr htmltools htmlwidgets igraph isoband jquerylib jsonlite knitr labeling lattice lifecycle listenv magrittr MASS Matrix matrixStats memoise mime parallelly pillar pkgconfig purrr R6 rappdirs rbibutils RColorBrewer Rcpp Rdpack rlang rmarkdown S7 sass scales stringi stringr systemfonts tibble tidyselect tinytex utf8 vctrs viridisLite visNetwork withr xfun yaml

flowGraph: Identifying differential cell populations in flow cytometry data accounting for marker frequency

Rendered fromflowGraph.Rmdusingknitr::rmarkdown

Last update: 2021-03-14
Started: 2020-09-28

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Readme and manuals

Help Manual

Help page	Topics
Determines the layer on which a phenotype resides.	cell_type_layers
Extracts markers from cell population phenotypes	extract_markers
Adds a feature.	fg_add_feature
Adds a feature summary.	fg_add_summary
Reformats phenotype	fg_clean_phen
Clears all featuresin a flowGraph object.	fg_clear_features
Removes all summary statistics.	fg_clear_summary
fg_data_fca	fg_data_fca
fg_data_pos2	fg_data_pos2
fg_data_pos30	fg_data_pos30
Extracts a set of phenotypes from a flowGraph object.	fg_extract_phenotypes
Clears all features and feature summaries in a flowGraph object.	fg_extract_raw
Extracts a set of samples from a flowGraph object.	fg_extract_samples
Converts cell counts into cumulated cell counts.	fg_feat_cumsum
Generates the proportion edge feature.	fg_feat_edge_prop
Generates the SpecEnr edge feature.	fg_feat_edge_specenr
Normalizes all features for class.	fg_feat_mean_class
Generates the proportion node feature.	fg_feat_node_prop
Generates the SpecEnr node feature.	fg_feat_node_specenr
Retrieves a feature matrix.	fg_get_feature
Retrieves and/or recalculates a feature description table.	fg_get_feature_desc
Retrieves feature summaries.	fg_get_feature_means
Retrieves a graph list from a given flowGraph object.	fg_get_graph
Retrieves the markers from a given flowGraph object.	fg_get_markers
Retrieves sample meta.	fg_get_meta
Retrieves a summary statistic.	fg_get_summary
Retrieves a feature summary description table.	fg_get_summary_desc
Retrieves the index of the requested summary.	fg_get_summary_index
Retrieves a table containing all node or edge summary statistics.	fg_get_summary_tables
Replace sample id's.	fg_gsub_ids
Replace marker names.	fg_gsub_markers
Load a flowGraph object from a specified folder path.	fg_load
Merges two flowGraph objects together.	fg_merge
Merges the samples from two flowGraph objects.	fg_merge_samples
Creates a cell hierarchy plot.	fg_plot
Creates a boxplot of the values of one node/edge	fg_plot_box
Creates a p value vs feature difference plot	fg_plot_pVSdiff
Creates a QQ plot of a summary statistic.	fg_plot_qq
Replaces sample meta.	fg_replace_meta
Removes a feature.	fg_rm_feature
Removes a feature summary.	fg_rm_summary
Saves flowGraph object to a specified path.	fg_save
Saves numerous plots for all summary statistics to a folder.	fg_save_plots
Determines cell hierarchy layout.	fg_set_layout
Calculates feature summary statistics.	fg_summary
flowGraph object constructor.	flowGraph
'flowGraph': A class for storing cell count feature values for the Phenotype class.	flowGraph-class show,flowGraph-method
flowGraph object constructor.	flowGraphSubset
Default for flowGraphSubset's summary_adjust	flowGraphSubset_summary_adjust
Default for flowGraphSubset's summary_pars	flowGraphSubset_summary_pars
Wrapper for map	fpurrr_map
Gets child populations of given cell populations	get_child
Gets edge proportions of a given edge matrix	get_eprop
Gets parent populations of given cell populations	get_paren
Creates edge lists.	get_phen_list
Genrates phenotype meta data.	get_phen_meta
Prepares a given node and edge graph list for plotting.	ggdf
Prepares parallel loop indices.	loop_ind_f
Normalizes matrix values by class.	mean_diff
Calcuate SpecEnr from proportion and expected proportion	ms_create
Determines which phenotypes are statistically significant	ms_psig
Plots a cell hierarchy.	plot_gr
Determines cell hierarchy layout.	set_layout_graph
Summarizes a numeric matrix.	summary_table
Converts input into a significance test function	test_c
Outputs elapsed time.	time_output
Formats time into string.	tstr

Package: flowGraph 1.21.0

flowGraph: Identifying differential cell populations in flow cytometry data accounting for marker frequency

Citation

Development and contributors

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)