generate_svg.R

library(tidyverse)
library(cowplot)
library(googlesheets)
library(dynbenchmark)

experiment("manual_ti")

# load in all datasets
datasets <- read_rds(derived_file("datasets.rds", "01-datasets/05-dataset_characterisation"))

run <- lst(
  dimred_id = "dp",
  person_id = "helenat",
  run_i = 1,
  run_id = glue::collapse(c(dimred_id, person_id, run_i), "_"),
  seed = sodium::data_encrypt(charToRaw(run_id), sodium::hash(charToRaw("robrecht")), nonce = sodium::hash(charToRaw("hi"), size = 24)) %>% rawToBits() %>% head(32) %>% packBits("integer") %>% abs()
)

if(file.exists(derived_file(paste0(run$run_id, ".rds")))) {
  run2 <- read_rds(derived_file(paste0(run$run_id, ".rds")))

  previous_dataset_ids <- run2$spaces %>% pull(id)
  new_dataset_ids <- datasets$id[!(datasets$id %in% previous_dataset_ids)]

  print("Previous run found, using previous ordering (plus extra datasets)")
  selected_datasets <- datasets %>% slice(match(c(previous_dataset_ids, new_dataset_ids), id))
} else {
  set.seed(run$seed)
  selected_datasets <- datasets %>% arrange(sample(n()))
}

##  ............................................................................
##  Generate svg for run                                                    ####

source("../dynmodular/dimred_wrappers.R")
dimred_function <- get(paste0("dimred_", run$dimred_id))

##  ............................................................................
##  Plot cells                                                              ####

load <- function(x) {
  if(class(x) == "matrix") {
    x
  } else {
    x()
  }
}

spaces <- map(seq_len(nrow(selected_datasets)), function(dataset_i) {
  # dataset <- extract_row_to_list(datasets %>% filter(category == "real"), 21)
  dataset <- extract_row_to_list(selected_datasets, dataset_i)
  print(dataset$id)

  dataset$expression <- load(dataset$expression)

  plots <- list()

  set.seed(run$seed)
  if (dataset$dataset_group == "control") {
    space <- dataset$space
  } else {
    space <- tryCatch(
      {dimred_function(dataset$expression)},
      error = function(x) dimred_pca(dataset$expression)
    )
    space <- space %>% as.data.frame() %>% tibble::rownames_to_column("cell_id")
  }

  plot <- ggplot(space) +
    geom_point(aes(Comp1, Comp2), alpha = 0.5) +
    ggraph::theme_graph() +
    theme(panel.border = element_rect(colour = "black", fill = NA, size = 1), plot.margin = margin(0, 0, 0, 0))


  tibble(
    plot = list(plot),
    id = dataset$id,
    x_scale = max(space$Comp1) - min(space$Comp1),
    y_scale = max(space$Comp2) - min(space$Comp2),
    x_shift = min(space$Comp1),
    y_shift = min(space$Comp2),
    space = list(as.data.frame(space))
  )
}) %>% bind_rows() %>% mutate(box_id = row_number())



##  ............................................................................
##  Create svg                                                              ####

# save png
base_size <- 2.5
plots <- spaces$plot
ncol <- 5
nrow <- ceiling(length(plots)/ncol)
plots %>%
  cowplot::plot_grid(plotlist = ., ncol = 5) %>%
  cowplot::save_plot(derived_file(glue::glue("{run$run_id}.png")), ., base_width = base_size*ncol, base_height = nrow * base_size, limitsize = F)

# save svg
if(!file.exists(derived_file(glue::glue("{run$run_id}.svg")))) {
  svg <- glue::glue(
    "
<?xml version = '1.0' standalone = 'no'?>
<!DOCTYPE svg PUBLIC '-//W3C//DTD SVG 1.1//EN'
  'http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd'>
<svg width = '{ncol*base_size}cm' height = '{nrow*base_size}cm' version = '1.1'
     xmlns = 'http://www.w3.org/2000/svg' xmlns:xlink= 'http://www.w3.org/1999/xlink'>
<g inkscape:label = 'back' sodipodi:insensitive = 'true' inkscape:groupmode = 'layer'>
<image xlink:href = '{run$run_id}.png' x = '0' y = '0' width = '{ncol*base_size}cm' height = '{nrow*base_size}cm' />
</g>
<g inkscape:label = 'segments' inkscape:groupmode = 'layer'>
</g>

</svg>
")
  svg %>% xml2::read_xml() %>% xml2::write_xml(derived_file(glue::glue("{run$run_id}.svg")))
} else {
  svg <- xml2::read_xml(derived_file(glue::glue("{run$run_id}.svg")))
  xml2::xml_find_first(svg, ".//svg:image")
  xml2::xml_replace(xml2::xml_find_first(svg, ".//svg:image"), glue::glue("<svg:image xlink:href = '{run$run_id}.png' x = '0' y = '0' width = '{ncol*base_size}cm' height = '{nrow*base_size}cm' />"), .copy = FALSE)
  xml2::xml_attr(svg, "width") <- glue::glue("{ncol*base_size}cm")
  xml2::xml_attr(svg, "height") <- glue::glue("{nrow*base_size}cm")
  svg %>% xml2::write_xml(derived_file(glue::glue("{run$run_id}.svg")))

  print("Not recreating svg")
}


##  ............................................................................
##  Save run info                                                           ####
run$base_size <- base_size
run$ncol <- ncol
run$nrow <- nrow
run$spaces <- select(spaces, -plot) # the plots are enormous (pryr::object_size(spaces$plot))
run %>% write_rds(derived_file(paste0(run$run_id, ".rds")))