workflowr::wflow_remove("analysis/direction-selected-analysis.Rmd")

analysis/direction-selected-analysis.Rmd

----
-title: "Direction selected analysis"
-output: html_document
----
-
-```{r setup, include=FALSE}
-knitr::opts_chunk$set(echo = TRUE)
-```
-
-```{r libraries, message = FALSE, warning = FALSE}
-library(dplyr)
-library(tibble)
-library(ggplot2)
-library(tidyr)
-library(patchwork)
-library(forcats)
-
-source(here::here("code", "analysis-utils.R"))
-source(here::here("code", "plot-utils.R"))
-```
-
-```{r functions}
-plot_prop_up <- function(data, data_id) {
-  stopifnot("prop_up" %in% colnames(data))
-  
-  data_label <- dataset_lookup[data_id]
-  
-  plot_data <- data %>% 
-    filter(data_id == !!data_id) %>% 
-    select(pars, cluster, prop_up) %>% 
-    mutate(plot_pars = pars_lookup[pars]) %>% 
-    mutate(plot_pars = fct_reorder(factor(plot_pars), prop_up, .fun = mean)) %>% 
-    select(cluster, plot_pars, prop_up)
-  
-  rm(data) 
-  
-  ggplot(plot_data, aes(x = cluster, y = plot_pars)) +
-    geom_tile(aes(fill = prop_up), colour = "black") + 
-    scale_fill_distiller(palette = "RdYlBu", direction = -1) + 
-    theme_bw() + 
-    labs(
-      x = "Cell type", 
-      y = "", 
-      fill = "Proportion\nupregulated\n",
-      title = paste0(data_label, " data")
-    ) + 
-    theme(
-      panel.grid.major = element_blank(),
-      panel.grid.minor = element_blank(),
-      panel.border = element_blank(),
-      axis.ticks.y = element_blank(),
-      axis.text.x = element_text(angle = 45, vjust = 0.9, hjust = 1)
-    )
-}
-```
-
-#  Load data
-
-```{r load-data}
-all_datasets_results <- load_real_data_results("all") 
-
-prop_up_data <- all_datasets_results %>% 
-  rowwise() %>% 
-  mutate(
-    top_mgs = list(get_top_sel_mgs(mgs, n = 20)), 
-    n_top_mgs = nrow(top_mgs),
-    n_up = nrow(filter(top_mgs, log_fc > 0 | raw_statistic > 0)),
-    prop_up = n_up / n_top_mgs
-  ) %>%  
-  ungroup()
-```
-
-# pbmc3k
-
-```{r pbmc3k-prop-up}
-pbmc3k_prop_up <- plot_prop_up(prop_up_data, "pbmc3k")
-pbmc3k_prop_up
-
-saveRDS(pbmc3k_prop_up, here::here("figures", "raw", "pbmc3k-prop-up.rds"))
-```
-
-# Lawlor
-
-```{r lawlor-prop-up}
-plot_prop_up(prop_up_data, "lawlor")
-```
-
-# Endothelial
-
-```{r endothelial-prop-up}
-plot_prop_up(prop_up_data, "endothelial")
-```
-
-# Zeisel
-
-```{r zeisel-prop-up}
-plot_prop_up(prop_up_data, "zeisel")
-```
-
-# Paul
-
-```{r paul-prop-up}
-plot_prop_up(prop_up_data, "paul")
-```
-
-# Mesenchymal
-
-```{r mesenchymal-prop-up}
-plot_prop_up(prop_up_data, "mesenchymal")
-```
-
-# SMART-seq3 pbmc
-
-```{r ss3-pbmc-prop-up}
-plot_prop_up(prop_up_data, "ss3_pbmc")
-```
-
-# CITE-seq
-
-```{r cite-seq-prop-up}
-plot_prop_up(prop_up_data, "citeseq")
-```
-
-# Astrocyte
-
-```{r astrocyte-prop-up}
-prop_up_data %>% 
-  mutate(cluster = astrocyte_clusters_lookup[cluster]) %>% 
-  plot_prop_up("astrocyte")
-```
-
-# Zhao
-
-```{r zhao-prop-up}
-plot_prop_up(prop_up_data, "zhao")
-```
-
-# Overall 
-
-```{r overall-prop-up}
-overall_prop_up <- prop_up_data %>% 
-  select(pars, data_id, cluster, prop_up) %>%
-  group_by(pars, data_id) %>% 
-  summarise(prop_up = mean(prop_up), .groups = "drop") %>% 
-  mutate(
-    plot_pars = pars_lookup[pars],
-    plot_dataset = dataset_lookup[data_id]
-  ) %>% 
-  mutate(plot_pars = fct_reorder(factor(plot_pars), prop_up, .fun = mean)) %>% 
-  ggplot(aes(x = plot_dataset, y = plot_pars)) +
-  geom_tile(aes(fill = prop_up), colour = "black") + 
-  scale_fill_distiller(palette = "RdYlBu", direction = -1) + 
-  theme_bw() + 
-  labs(
-    x = "Dataset", 
-    y = "", 
-    fill = "Proportion\nupregulated\n",
-  ) + 
-  theme(
-    panel.grid.major = element_blank(),
-    panel.grid.minor = element_blank(),
-    panel.border = element_blank(),
-    axis.ticks.y = element_blank(),
-    axis.text.x = element_text(angle = 45, vjust = 1, hjust = 1)
-  )
-overall_prop_up
-
-saveRDS(overall_prop_up, here::here("figures", "raw", "overall-prop-up.rds"))
-```