Last updated: 2021-02-16

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Knit directory: mage_2020_marker-gene-benchmarking/

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File Version Author Date Message
html 2863555 Jeffrey Pullin 2021-02-10 Build site.
Rmd ffe660c Jeffrey Pullin 2021-02-09 Update 9/2/2021

library(tibble)
library(dplyr)
library(ggplot2)
library(tidyr)

Aim

Measure the time the different methods take to run.

Data loading

results_folder <- here::here("results")
file_names <- list.files(results_folder, full.names = TRUE)

times <- numeric(length(file_names))
for (i in seq_along(file_names)) {
  res <- readRDS(file_names[[i]])
  times[[i]] <- res$time
  rm(res)
}

# TODO: Refactor! Reduce the number of `separate()` calls.
time_data <- tibble(file_name = file_names, time = times) %>% 
  mutate(file_name = basename(file_names)) %>% 
  mutate(file_name = substr(file_name, 1, nchar(file_name) - 4)) %>% 
  separate(file_name, sep = "-", into = c("sim", "method")) %>% 
  separate(method, sep = "_", into = c("method_name", "pars"), extra = "merge") %>% 
  separate(sim, sep = "_", into = c("sim", "sim_id")) %>% 
  select(-sim)

Plots

scran

time_data %>% 
  filter(method_name == "scran") %>%
  ggplot(aes(x = pars, y = time)) +
  geom_point() + 
  labs(y = "Time (s)", x = "scran options") + 
  theme_bw()

Version Author Date
2863555 Jeffrey Pullin 2021-02-10

Seurat

time_data %>% 
  filter(method_name == "seurat") %>%
  ggplot(aes(x = pars, y = time)) +
  geom_point() + 
  labs(y = "Time (s)", x = "Test method") + 
  theme_bw() + 
  theme(axis.text.x = element_text(angle = 45, hjust=1))

Version Author Date
2863555 Jeffrey Pullin 2021-02-10

All

time_data %>% 
  mutate(method = paste0(method_name, "-", pars)) %>% 
  ggplot(aes(x = method, y = time)) + 
  geom_point() + 
  labs(y = "Time (s)", x = "Parameters") + 
  theme_bw() + 
  theme(axis.text.x = element_text(angle = 45, hjust=1))

Version Author Date
2863555 Jeffrey Pullin 2021-02-10

All (fast)

time_data %>% 
  filter(time < 100) %>% 
  mutate(method = paste0(method_name, "-", pars)) %>% 
  ggplot(aes(x = method, y = time)) + 
  geom_point() + 
  labs(y = "Time (s)", x = "Parameters") + 
  theme_bw() + 
  theme(axis.text.x = element_text(angle = 45, hjust=1))

Version Author Date
2863555 Jeffrey Pullin 2021-02-10

Questions:

  • Why is Seurat’s Wilcox approximately three times as slow as scran’s?

Seurat uses limma’s implementation of wilcox.test which it suggests is faster than the function in base R (see the Seurat NEWS.md file). scran uses it’s own (R) implementation with some odd blocking stuff I don’t fully understand.


devtools::session_info()
─ Session info ───────────────────────────────────────────────────────────────
 setting  value                       
 version  R version 4.0.3 (2020-10-10)
 os       Red Hat Enterprise Linux    
 system   x86_64, linux-gnu           
 ui       X11                         
 language (EN)                        
 collate  en_AU.UTF-8                 
 ctype    en_AU.UTF-8                 
 tz       Australia/Melbourne         
 date     2021-02-16                  

─ Packages ───────────────────────────────────────────────────────────────────
 package     * version date       lib source        
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[1] /mnt/mcfiles/jpullin/R/x86_64-pc-linux-gnu-library/4.0
[2] /opt/R/4.0.3/lib/R/library