# prepare environment
source(snakemake@params$setup_code_fname)
devtools::load_all("../..")
# run model
clip_thres <- 10^-10
fit <- pareg::pareg(
study$df %>%
select(gene, pvalue) %>%
mutate(pvalue = ifelse(pvalue <= clip_thres, clip_thres, pvalue)),
df_terms
)
df <- fit %>%
as.data.frame() %>%
mutate(method = "pareg_clip", enrichment = abs(enrichment))
df %>%
arrange(desc(abs(enrichment))) %>%
head()
# misc
do.call(rbind, fit$obj$loss_hist) %>%
as_tibble() %>%
unnest(everything()) %>%
mutate(iteration = seq_along(fit$obj$loss_hist)) %>%
pivot_longer(-iteration) %>%
ggplot(aes(x = iteration, y = value, color = name)) +
geom_line() +
# geom_point() +
theme_minimal()
ggsave(
file.path(dirname(snakemake@output$fname), "loss.pdf"),
width = 8,
height = 6
)
# save result
df %>%
write_csv(snakemake@output$fname)
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