Title

Title

plot_DE_volcano(
  x,
  chromosomes = paste0("chr", c(1:22, "X", "Y")),
  annotate_top = 5,
  cut_pvalue = 0.001,
  cut_lfc = 0.25
)

Arguments

cut_lfc

Value

Examples

x = Rcongas::congas_example

print(x)
#> ── [ Rcongas ]  ────────────────────────────────────────────────────────────────
#> 
#> → Data: 503 cells with 8564 genes, aggregated in 70 segments.
#> 
#> ℹ Clusters: k = 2, model with AIC = 577427.35.
#> 
#> ● Cluster c1, n = 379 [75.35% of total cells].
#> ● Cluster c2, n = 124 [24.65% of total cells].
#> 
#> ── CNA highlights (alpha = 0.05) 
#> 
#> ✔  c1 CNA(s):  [chr14:93300001:105450000] vs c2, [chr15:67050001:102600000] vs c2, [chr16:1:3750000] vs c2, and [chr18:32400001:55950000] vs c2
#> 
#> 
#> ── Differential Expression DESeq2  (1 vs 2) 
#> ✔ 212 DE genes (alpha = 0.01, |lfc| > 0.25).

# Shows all data available
plot_DE_volcano(x)


# More stringent parameters, annotate more genes
plot_DE_volcano(x, cut_pvalue = 1e-5, annotate_top = 10)


# More stringent parameters and resitrict chromosome
plot_DE_volcano(x, cut_lfc = 2, chromosomes = c("chr1", "chr2"))
#> Warning: Removed 2 rows containing missing values (geom_vline).