Package index • cyCONDOR

Data Loading

Functions to load data to a condor object.

prep_fcd(): prep_fcd

prep_fjw(): Read FlowJo Workspace

transform_data(): transform_data

clr(): crt_transform

read_data(): read_data

Dimensionality Reduction

Dimensionality reduction functions.

runPCA_pseudobulk(): runPCA_pseudobulk

runPCA(): runPCA

runUMAP(): runUMAP

runtSNE(): runtSNE

runDM(): runDM

Clustering

Clustering functions.

runPhenograph(): runPhenograph

runFlowSOM(): runFlowSOM

metaclustering(): metaclustering

Batch Correction

Implementation of Harmony.

harmonize_PCA(): harmonize_PCA

harmonize_intensities(): harmonize_intensities

train_cytonorm(): train_cytonorm

run_cytonorm(): run_cytonorm

Pseudotime

Implementation of slingshot.

runPseudotime(): Function of calculate Pseudotime from HDFC data analysed with cyCONDOR

Classifier and Data Projection

Machine learning classifier and data projection.

train_classifier_model(): Train a machine learning classifier for the clinical classification of HDFC data.

train_transfer_model(): train_transfer_model

predict_classifier(): Predict clinical classification.

predict_labels(): predict_labels

learnUMAP(): learnUMAP

runAstir_cellstates(): runAstir_cellstates

runAstir_celltype(): Run Astir cell type prediction

Data Visualization

Collection of functions to visualize the results.

getTable(): Get summary values

PC_loadings(): PC_loadings

plot_frequency_boxplot(): box plot of cell population frequencies

plot_frequency_barplot(): bar chart of cell population frequencies

plot_counts_barplot(): bar chart of cell population counts

plot_confusion_HM(): plot_confusion_HM

confusionMatrix(): confusionMatrix

plot_marker_density(): density plot of marker expression in cell populations grouped by a meta variable

plot_marker_group_HM(): Heatmap of scaled expression to compare two groups

plot_marker_HM(): Heatmap of scaled expression by cell population

plot_dim_density(): dimensionality reduction plot with density distribution

plot_dim_red(): Dimensionality reduction dotplot

plot_marker_violinplot(): violin plot of marker expression in cell populations

plot_marker_boxplot(): plot box plots of marker median or mean

plot_marker_dotplot(): plot_marker_dotplot

plot_marker_ridgeplot(): ridgeline plot of marker expression in cell populations

Differential Testing

Collection of functions to calculate differential abundance and expression.

frequency_anova_test(): Anova test to compare cell population frequencies of independent samples

frequency_friedman_test(): Friedman Rank Sum test to compare cell population frequencies of paired samples

frequency_kruskal_test(): Kruskal-Wallis test to compare cell population frequencies

frequency_t_test(): t-test to compare cell population frequencies

frequency_wilcox_test(): Wilcoxon test to compare cell population frequencies

prepInputDiffcyt(): Convert a condor object to se object

marker_wilcox_test(): Differential expression testing on cell level

add_diffcyt_statistics(): Add statistical results from the diffcyt package to the fcd.

Utilities

Collection of misc functions.

scaleColors(): scaleColors

used_markers(): used_markers

change_param_name(): change_param

check_IDs(): check_IDs

df_frequency(): df_frequency

filter_fcd(): filter_fcd

merge_condor(): merge_condor

subset_fcd(): subset_fcd

subset_fcd_byparam(): subset_fcd_byparam

subsample_geosketch(): Subsampling base on geometric sketching

checkInput(): Helper function within cyCONDOR

measured_markers(): measured_markers

create_metaclustering_script(): create_metaclustering_script

condor_session_info(): condor_session_info

corr_plot_comparison(): Sample-wise correlation of cell type proportions to compare manual gating and cyCONDOR.

write_fcs(): Save the results from cyCONDOR as FCS file(s)

condor_info(): condor_info

export_sce(): Export Flow Cytometry Dataset as SCE.

order_param(): order_param