ewce_plot {EWCE}

R Documentation

Plot EWCE results

Description

ewce_plot generates plots of EWCE enrichment results

Usage

ewce_plot(total_res, mtc_method = "bonferroni", ctd = NULL)

Arguments

total_res	results dataframe generated using bootstrap_enrichment_test or ewce_expression_data functions. Multiple results tables can be merged into one results table, as long as the 'list' column is set to distinguish them.
mtc_method	method to be used for multiple testing correction. Argument is passed to p.adjust. Valid options are "holm", "hochberg", "hommel", "bonferroni", "BH", "BY",
ctd	Should be provided so that the dendrogram can be taken from it and added to plots

Value

A ggplot containing the plot

Examples

library(ewceData)
# Load the single cell data
ctd <- ctd()

# Set the parameters for the analysis
# Use 3 bootstrap lists for speed, for publishable analysis use >10000
reps <- 3

# Load the gene list and get human orthologs
example_genelist <- example_genelist()
mouse_to_human_homologs <- mouse_to_human_homologs()
m2h <- unique(mouse_to_human_homologs[, c("HGNC.symbol", "MGI.symbol")])
mouse.hits <-
     unique(m2h[m2h$HGNC.symbol %in% example_genelist, "MGI.symbol"])
mouse.bg <- unique(c(m2h$MGI.symbol[1:100],mouse.hits))

# Bootstrap significance test, no control for transcript length or GC content
full_results <- bootstrap_enrichment_test(
    sct_data = ctd, hits = mouse.hits,
    bg = mouse.bg, reps = reps, annotLevel = 2,
    sctSpecies = "mouse", genelistSpecies = "mouse"
)

# Generate the plot
print(ewce_plot(full_results$results, mtc_method = "BH"))

---