Visualize query results as a composite manhattan/density plot.

Visualize query results as a composite manhattan/density plot.

plotQueryResultsManh(queryResults, doPlot = TRUE)

Arguments

queryResults

A list containing the results of a query performed with queryWithContrasts

doPlot

Logical scalar specifying if a plot should be generated.

Value

A composite manhattan/density plot for the scores of queries using different contrast components against the respective contrast DBs.

Author

Panagiotis Papasaikas, Michael Stadler

Examples

MKL1_human <- readRDS(system.file("extdata", "GSE215150_MKL1_Human.rds",
package = "orthos"))

# Decompose contrasts:
dec_MKL1_human <- decomposeVar(M = MKL1_human, treatm = c(2, 3), cntr = c(1, 1), 
                              organism = "Human", verbose = FALSE)
#> see ?orthosData and browseVignettes('orthosData') for documentation
#> loading from cache
#> see ?orthosData and browseVignettes('orthosData') for documentation
#> loading from cache
#> see ?orthosData and browseVignettes('orthosData') for documentation
#> loading from cache

# Perform query against contrast DB with the decomposed fractions.
# !!!Note!!! mode="DEMO" for demonstration purposes only.                             
params <- BiocParallel::MulticoreParam(workers = 2)                              
query.res.human <- queryWithContrasts(dec_MKL1_human, organism = "Human", 
                                     BPPARAM = params, verbose = FALSE, 
                                     mode = "DEMO")
#> demo_decomposed_contrasts_human_rds  already present in cache at: /Users/runner/Library/Caches/org.R-project.R/R/ExperimentHub/human_v212_NDF_c100_DEMOse.rds
#> demo_decomposed_contrasts_human_hdf5  already present in cache at: /Users/runner/Library/Caches/org.R-project.R/R/ExperimentHub/human_v212_NDF_c100_DEMOassays.h5

                                     
# plot results for individual contrasts using composite Manhattan/Density plots:
ManhDensPlots <- plotQueryResultsManh(query.res.human, doPlot = FALSE)
ManhDensPlots[["caMKL1"]]