Hardcoded pvalue in plot
In the MA plot section "MA and Volcano plots" the description reads:
Each gene is represented with a dot. Genes with an adjusted p value below a certain threshold are shown in cyan (True)
However the code for adding color is using pvalue
instead of padj
and uses a harcoded value of 0.05
:
https://git.mpi-cbg.de/bioinfo/ngs_tools/blob/master/dge_workflow/featcounts_deseq_mf.R#L576
deResults %>% ggplot(aes(0.5 * log2(mean_norm_count_1 * mean_norm_count_2), log2(mean_norm_count_2 / mean_norm_count_1), color = pvalue < 0.05)) +
geom_point(alpha = 0.1) +
geom_hline(yintercept = 0, color = "red") +
facet_grid(condition_1 ~ condition_2)
Expected behaviour
Genes coloured by is_hit
which reflects the cut-off used in arguments (qcutoff
or pcutoff
).