Package: flowGraph 1.15.0

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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flowGraph.pdf |flowGraph.html✨
flowGraph/json (API)
NEWS

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

Peer review:

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

Datasets:

On BioConductor:flowGraph-1.13.0(bioc 3.20)flowGraph-1.12.0(bioc 3.19)

flowcytometrystatisticalmethodimmunooncologysoftwarecellbasedassaysvisualization

4.00 score 10 scripts 134 downloads 50 exports 73 dependencies

Last updated 23 days agofrom:dd112bfb04. Checks:OK: 1 NOTE: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 30 2024
R-4.5-winNOTEOct 30 2024
R-4.5-linuxNOTEOct 30 2024
R-4.4-winNOTEOct 30 2024
R-4.4-macNOTEOct 30 2024
R-4.3-winNOTEOct 30 2024
R-4.3-macNOTEOct 30 2024

Exports:cell_type_layersfg_add_featurefg_add_summaryfg_clear_featuresfg_clear_summaryfg_extract_phenotypesfg_extract_rawfg_extract_samplesfg_feat_edge_propfg_feat_edge_specenrfg_feat_mean_classfg_feat_node_propfg_feat_node_specenrfg_get_featurefg_get_feature_descfg_get_feature_meansfg_get_graphfg_get_markersfg_get_metafg_get_summaryfg_get_summary_descfg_get_summary_indexfg_get_summary_tablesfg_gsub_idsfg_gsub_markersfg_loadfg_mergefg_merge_samplesfg_plotfg_plot_boxfg_plot_pVSdifffg_plot_qqfg_replace_metafg_rm_featurefg_rm_summaryfg_savefg_save_plotsfg_set_layoutfg_summaryflowGraphflowGraphSubsetflowGraphSubset_summary_adjustflowGraphSubset_summary_parsget_phen_listget_phen_metaggdfplot_grset_layout_graphshowsummary_table

Dependencies:base64encbslibcachemclicodetoolscolorspacecpp11data.tabledigesteffsizeevaluatefansifarverfastmapfontawesomefsfurrrfutureggiraphggplot2ggrepelglobalsgluegridExtragtablehighrhtmltoolshtmlwidgetsigraphisobandjquerylibjsonliteknitrlabelinglatticelifecyclelistenvmagrittrMASSMatrixmatrixStatsmemoisemgcvmimemunsellnlmeparallellypillarpkgconfigpurrrR6rappdirsrbibutilsRColorBrewerRcppRdpackrlangrmarkdownsassscalesstringistringrsystemfontstibbletinytexutf8uuidvctrsviridisLitevisNetworkwithrxfunyaml

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

Alice Yue

Rendered fromflowGraph.Rmdusingknitr::rmarkdownon Oct 30 2024.

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

Readme and manuals

Help Manual

Help pageTopics
Determines the layer on which a phenotype resides.cell_type_layers
Extracts markers from cell population phenotypesextract_markers
Adds a feature.fg_add_feature
Adds a feature summary.fg_add_summary
Reformats phenotypefg_clean_phen
Clears all featuresin a flowGraph object.fg_clear_features
Removes all summary statistics.fg_clear_summary
fg_data_fcafg_data_fca
fg_data_pos2fg_data_pos2
fg_data_pos30fg_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/edgefg_plot_box
Creates a p value vs feature difference plotfg_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_adjustflowGraphSubset_summary_adjust
Default for flowGraphSubset's summary_parsflowGraphSubset_summary_pars
Wrapper for mapfpurrr_map
Gets child populations of given cell populationsget_child
Gets edge proportions of a given edge matrixget_eprop
Gets parent populations of given cell populationsget_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 proportionms_create
Determines which phenotypes are statistically significantms_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 functiontest_c
Outputs elapsed time.time_output
Formats time into string.tstr