plot differentially accessible peaks for a given comparison
heatmap_differential(results, comparison = NULL, ...)Arguments
- results
cinaR result object
- comparison
these are created by cinaR from `contrasts` user provided. If not selected the first comparison will be shown!
- ...
additional arguments for heatmap function, for more info `?pheatmap`
Value
ggplot object
Examples
# \donttest{
library(cinaR)
data(atac_seq_consensus_bm) # calls 'bed'
# a vector for comparing the examples
contrasts <- sapply(strsplit(colnames(bed), split = "-", fixed = TRUE),
function(x){x[1]})[4:25]
results <- cinaR(bed, contrasts, reference.genome = "mm10")
#> >> Experiment type: ATAC-Seq
#> >> Matrix is filtered!
#> >> preparing features information... 2022-05-06 16:30:32
#> >> identifying nearest features... 2022-05-06 16:30:32
#> >> calculating distance from peak to TSS... 2022-05-06 16:30:32
#> >> assigning genomic annotation... 2022-05-06 16:30:32
#> >> assigning chromosome lengths 2022-05-06 16:30:34
#> >> done... 2022-05-06 16:30:34
#> >> Method: edgeR
#> FDR:0.05& abs(logFC)<0
#> >> Estimating dispersion...
#> >> Fitting GLM...
#> >> DA peaks are found!
#> >> No `geneset` is specified so immune modules (Chaussabel, 2008) will be used!
#> >> enrichment.method` is not selected. Hyper-geometric p-value (HPEA) will be used!
#> >> Mice gene symbols are converted to human symbols!
#> >> Enrichment results are ready...
#> >> Done!
heatmap_differential(results)
#> Warning: 'comparison' is not set so 'B6_NZO' will be used!
# }