Function reference • Rubrary

Exploratory data analysis

plot_distribution(): Plot distribution of numeric vector

plot_density(): Density plot by group

plot_scatter(): Plot simple scatter

get_kspval(): Calculate (signed) Kolgomorov-Smirnov enrichment p-value in dataframe

check_normal(): Shapiro-Wilk test of normality

calc_sumZscore(): Generate Sum Z Score

run_RRHO(): Run RRHO analysis

phyper_df(): Hypergeometric test, 0 vs. non-0, on columns of a dataframe

Principal components analysis (PCA)

run_PCA(): Run PCA (prcomp wrapper)

plot_PCA(): Plot PCA with annotation

plot_PCA_matrix(): Plot PCA matrix via GGally::ggpairs

plot_PCA_3D(): Plot 3D PCA scores/loadings via plotly

plot_PCA_biplot(): Plot PCA biplot

get_loadings(): Extract loadings from prcomp object

plot_screeplot(): Plot screeplot from prcomp

rotate_varimax(): Apply varimax rotation to PCA scores

predict_PCA(): PCA prediction by projecting query/test samples onto PCA of reference/train samples

Differentially expressed genes (DESeq)

output_DESeq(): Output DESeq results as dataframe with signed log p metric

plot_DEgene_boxplot(): Plot gene expression boxplots of selected genes (from DESeq signature)

plot_waterfall(): Plot horizontal waterfall plot (with optional density)

plot_volcano(): Plot (DE genes) volcano plot

Gene set enrichment analysis (GSEA)

Including GSEA Squared functions.

format_GSEA_name(): Format GSEA pathway name

plot_GSEA_barplot(): Plot GSEA NES barplot

plot_GSEA_pathway(): Plot GSEA pathway plots (waterfall + enrichment)

plot_GSEA_pathway_batch(): plot_GSEA_pathway wrapper that works nicely with lapply

get_GSEAsq_terms(): Get GSEA Squared terms/keywords

run_GSEA_squared(): Run GSEA Squared on GSEA results

plot_GSEAsq_density(): Plot categorical percentile rank comparison between two GSEA squared signatures

Single cell RNA analysis

Seurat object based analysis and visualization.

plot_dimplot_grid(): Plot Seurat DimPlot grid set

plot_comp_barplot(): Plot stacked barplot filled by group

plot_featurescatter(): Plot FeatureScatter wrapper

assess_integration() run_LISI() run_MixingMetric() run_CellMixS(): Compute and plot integration assessment cell-specific methods for Seurat object

genecoexp_scatter_hyper(): Plot pairwise gene coexpression scatter and calculate hypergeometric enrichment p-value between two genelists

Gene manipulation

convert_genes(): Convert list of genes via BioMart

get_PC_genes(): Retrieve protein coding genes from Ensembl BioMart

filter_genes(): Filter dataframe by list of (protein coding) genes

get_gene_desc(): Get gene description from BioMart

quantile_norm(): Quantile normalization, upper quartile by default

get_log_coding_geneexp(): Get log(x+1) protein coding gene expression matrix

Utility

Miscellaneous helper functions.

rread(): Wrapper for data.table::fread implementing row.names functionality

rwrite(): Wrapper for data.table::fwrite with tab separated values (TSV) default parameters

corner(): Like head but just the corner

split_line(): Split text into multiple lines

full_join_rownames(): Full join by rownames

left_join_rownames(): Left join by rownames

cbind(<fill>): Combine data.frames by column, filling in missing rows.

use_pkg(): Check if package is installed, prompt if not

inst_pkg(): Prompt user to install package

reload_pkg(): Reload package by installation path

Data

Used for vignettes and examples.

airway_deseq_res: Airway Dex Treated vs. Untreated DESeq2 Results

GSEA_pathways: Pathways from msigdbr to use with fgsea