Man pages for aya49/flowGraph
Identifying differential cell populations in flow cytometry data accounting for marker frequency
| cell_type_layers | Determines the layer on which a phenotype resides. |
| extract_markers | Extracts markers from cell population phenotypes |
| fg_add_feature | Adds a feature. |
| fg_add_summary | Adds a feature summary. |
| fg_clean_phen | Reformats phenotype |
| fg_clear_features | Clears all featuresin a flowGraph object. |
| fg_clear_summary | Removes all summary statistics. |
| fg_data_fca | fg_data_fca |
| fg_data_pos2 | fg_data_pos2 |
| fg_data_pos30 | fg_data_pos30 |
| fg_extract_phenotypes | Extracts a set of phenotypes from a flowGraph object. |
| fg_extract_raw | Clears all features and feature summaries in a flowGraph... |
| fg_extract_samples | Extracts a set of samples from a flowGraph object. |
| fg_feat_cumsum | Converts cell counts into cumulated cell counts. |
| fg_feat_edge_specenr | Generates the SpecEnr edge feature. |
| fg_feat_mean_class | Normalizes all features for class. |
| fg_feat_node_prop | Generates the proportion node feature. |
| fg_feat_node_specenr | Generates the SpecEnr node feature. |
| fg_feat_prop_edge | Generates the proportion edge feature. |
| fg_get_feature | Retrieves a feature matrix. |
| fg_get_feature_desc | Retrieves and/or recalculates a feature description table. |
| fg_get_feature_means | Retrieves feature summaries. |
| fg_get_graph | Retrieves a graph list from a given flowGraph object. |
| fg_get_markers | Retrieves the markers from a given flowGraph object. |
| fg_get_meta | Retrieves sample meta. |
| fg_get_summary | Retrieves a summary statistic. |
| fg_get_summary_desc | Retrieves a feature summary description table. |
| fg_get_summary_index | Retrieves the index of the requested summary. |
| fg_get_summary_tables | Retrieves a table containing all node or edge summary... |
| fg_gsub_ids | Replace sample id's. |
| fg_gsub_markers | Replace marker names. |
| fg_load | Load a flowGraph object from a specified folder path. |
| fg_merge | Merges two flowGraph objects together. |
| fg_merge_samples | Merges the samples from two flowGraph objects. |
| fg_plot | Creates a cell hierarchy plot. |
| fg_plot_box | Creates a boxplot of the values of one node/edge |
| fg_plot_pVSdiff | Creates a p value vs feature difference plot |
| fg_plot_qq | Creates a QQ plot of a summary statistic. |
| fg_replace_meta | Replaces sample meta. |
| fg_rm_feature | Removes a feature. |
| fg_rm_summary | Removes a feature summary. |
| fg_save | Saves flowGraph object to a specified path. |
| fg_save_plots | Saves numerous plots for all summary statistics to a folder. |
| fg_set_layout | Determines cell hierarchy layout. |
| fg_summary | Calculates feature summary statistics. |
| flowGraph | flowGraph object constructor. |
| flowGraph-class | 'flowGraph': A class for storing cell count feature values... |
| flowGraphSubset | flowGraph object constructor. |
| flowGraphSubset_summary_adjust | Default for flowGraphSubset's summary_adjust |
| flowGraphSubset_summary_pars | Default for flowGraphSubset's summary_pars |
| fpurrr_map | Wrapper for map |
| get_child | Gets child populations of given cell populations |
| get_eprop | Gets edge proportions of a given edge matrix |
| get_paren | Gets parent populations of given cell populations |
| get_phen_list | Creates edge lists. |
| get_phen_meta | Genrates phenotype meta data. |
| ggdf | Prepares a given node and edge graph list for plotting. |
| loop_ind_f | Prepares parallel loop indices. |
| meandiff | Normalizes matrix values by class. |
| ms_create | Calcuate SpecEnr from proportion and expected proportion |
| ms_psig | Determines which phenotypes are statistically significant |
| plot_gr | Plots a cell hierarchy. |
| set_layout_graph | Determines cell hierarchy layout. |
| summary_table | Summarizes a numeric matrix. |
| test_c | Converts input into a significance test function |
| time_output | Outputs elapsed time. |
| tstr | Formats time into string. |
