Zero p-values
Last updated: 2024-01-01
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Knit directory:
mage_2020_marker-gene-benchmarking/
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library(SingleCellExperiment)
library(dplyr)
library(ggplot2)
library(tibble)
library(purrr)
library(forcats)
library(topconfects)
library(patchwork)
library(tidyr)
source(here::here("code", "analysis-utils.R"))
source(here::here("code", "plot-utils.R"))real_data_data <- retrieve_real_data_parameters() %>%
rowwise() %>%
mutate(mgs = list(readRDS(full_filename)$result)) %>%
ungroup()
pbmc3k <- readRDS(here::here("data", "real_data", "zeisel.rds"))real_data_data %>%
filter(data_id == "endothelial") %>%
filter(method != "rankcorr", method != "difference", method != "lm",
pars != "seurat_roc", method != "random") %>%
rowwise() %>%
mutate(n_zero = nrow(filter(mgs, p_value == 0))) %>%
ungroup() %>%
mutate(pars_plot = pars_lookup[pars]) %>%
mutate(pars_plot = fct_reorder(factor(pars_plot), n_zero)) %>%
ggplot(aes(pars_plot, n_zero)) +
geom_col(fill = "seagreen") +
coord_flip() +
labs(y = "Number of 0 p-values",
x = "Method",
title = "Number of 0 p-values - Endothelial data") +
theme_bw()
real_data_data %>%
filter(data_id == "zeisel") %>%
filter(method != "rankcorr", method != "difference", method != "lm",
pars != "seurat_roc", method != "random", pars != "seurat_poisson") %>%
rowwise() %>%
mutate(n_zero = nrow(filter(mgs, p_value == 0))) %>%
ungroup() %>%
mutate(pars_plot = pars_lookup[pars]) %>%
mutate(pars_plot = fct_reorder(factor(pars_plot), n_zero)) %>%
ggplot(aes(pars_plot, n_zero)) +
geom_col(fill = "seagreen") +
coord_flip() +
labs(y = "Number of 0 p-values",
x = "Method",
title = "Number of 0 p-values - Zeisel data") +
theme_bw()
real_data_data %>%
filter(data_id == "pbmc3k") %>%
filter(method != "rankcorr", method != "difference", method != "lm",
pars != "seurat_roc", method != "random", pars != "seurat_poisson") %>%
rowwise() %>%
mutate(n_zero = nrow(filter(mgs, p_value == 0))) %>%
ungroup() %>%
mutate(pars_plot = pars_lookup[pars]) %>%
mutate(pars_plot = fct_reorder(factor(pars_plot), n_zero)) %>%
ggplot(aes(pars_plot, n_zero)) +
geom_col(fill = "seagreen") +
coord_flip() +
labs(y = "Number of 0 p-values",
x = "Method",
title = "Number of 0 p-values - pbmc3k data") +
theme_bw()
seurat_wilcox_zeisel <- readRDS(
here::here("results", "real_data", "zeisel-seurat_wilcox.rds")
)
scanpy_wilcoxon_tc_zeisel <- readRDS(
here::here("results", "real_data", "zeisel-scanpy_wilcoxontiecorrect_rankby_raw.rds")
)scanpy_genes <- scanpy_wilcoxon_tc_zeisel %>%
pluck("result") %>%
filter(cluster == "oligodendrocytes") %>%
get_top_sel_mgs(n = 40) %>%
pull("gene")
seurat_genes <- seurat_wilcox_zeisel %>%
pluck("result") %>%
filter(cluster == "oligodendrocytes") %>%
get_top_sel_mgs(n = 40) %>%
pull("gene")
rank_rank_plot(
scanpy_genes,
seurat_genes,
"Scanpy Wilcoxon TC (rankby_abs)",
"Seurat Wilcox"
) +
ggtitle("Scanpy vs Seurat Wilcoxon (zero p-values)")
all_datasets_results <- retrieve_real_data_parameters() %>%
rowwise() %>%
mutate(
mgs_raw = list(readRDS(full_filename)$result),
mgs = list(split(mgs_raw, mgs_raw$cluster))
) %>%
ungroup() %>%
unnest_longer(
col = mgs,
values_to = "mgs",
indices_to = "cluster"
)scanpy_seurat_zeisel_oligodendrocytes <- all_datasets_results %>%
mutate(n = 125) %>%
filter(data_id == "zeisel") %>%
filter(
pars %in% c("scanpy_wilcoxontiecorrect_rankby_abs", "seurat_wilcox")
) %>%
filter(cluster == "oligodendrocytes") %>%
rowwise() %>%
mutate(mgs = list(get_top_sel_mgs(mgs, n = n))) %>%
mutate(
rank = list(1:n),
log_fc = list(mgs$log_fc),
p_value = list(mgs$p_value),
zero_p_value = list(p_value == 0)
) %>%
mutate(plot_method = method_lookup[method]) %>%
unnest(cols = c(rank, log_fc, zero_p_value)) %>%
# Shrink plot file size.
select(-c(mgs, mgs_raw)) %>%
ggplot(aes(x = rank, y = log_fc, colour = zero_p_value)) +
geom_point() +
facet_wrap(~plot_method) +
labs(
x = "Gene rank",
y = "Log fold-change",
colour = "p-value = 0?",
) +
scale_colour_manual(values = c("black", "red")) +
theme_bw()
scanpy_seurat_zeisel_oligodendrocytes
saveRDS(
scanpy_seurat_zeisel_oligodendrocytes,
here::here("figures", "raw", "scanpy-seurat-zeisel-oligodendrocytes.rds")
)
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