... | ... |
@@ -1258,7 +1258,9 @@ cumulative_count_union <- function(x, |
1258 | 1258 |
#' default_stats() |
1259 | 1259 |
default_stats <- function() { |
1260 | 1260 |
list( |
1261 |
- diversity = vegan::diversity, |
|
1261 |
+ shannon = ~ vegan::diversity(.x, index = "shannon"), |
|
1262 |
+ simpson = ~ vegan::diversity(.x, index = "simpson"), |
|
1263 |
+ invsimpson = ~ vegan::diversity(.x, index = "invsimpson"), |
|
1262 | 1264 |
sum = ~ sum(.x, na.rm = TRUE), |
1263 | 1265 |
count = length, |
1264 | 1266 |
describe = ~ tibble::as_tibble(psych::describe(.x)) |
... | ... |
@@ -254,6 +254,7 @@ import_association_file <- function(path, |
254 | 254 |
filter_for = NULL, |
255 | 255 |
import_iss = FALSE, |
256 | 256 |
export_widget_path = NULL, |
257 |
+ convert_tp = TRUE, |
|
257 | 258 |
...) { |
258 | 259 |
# Check parameters |
259 | 260 |
stopifnot(is.character(path) & length(path) == 1) |
... | ... |
@@ -310,55 +311,45 @@ import_association_file <- function(path, |
310 | 311 |
missing_dates |
311 | 312 |
))) |
312 | 313 |
## Fix timepoints |
313 |
- if (!"TimepointMonths" %in% colnames(as_file)) { |
|
314 |
- as_file <- as_file %>% |
|
315 |
- tibble::add_column(TimepointMonths = NA_real_) |
|
316 |
- } |
|
317 |
- if (!"TimepointYears" %in% colnames(as_file)) { |
|
314 |
+ if (convert_tp) { |
|
315 |
+ if (!"TimepointMonths" %in% colnames(as_file)) { |
|
316 |
+ as_file <- as_file %>% |
|
317 |
+ tibble::add_column(TimepointMonths = NA_real_) |
|
318 |
+ } |
|
319 |
+ if (!"TimepointYears" %in% colnames(as_file)) { |
|
320 |
+ as_file <- as_file %>% |
|
321 |
+ tibble::add_column(TimepointYears = NA_real_) |
|
322 |
+ } |
|
318 | 323 |
as_file <- as_file %>% |
319 |
- tibble::add_column(TimepointYears = NA_real_) |
|
320 |
- } |
|
321 |
- as_file <- as_file %>% |
|
322 |
- dplyr::mutate( |
|
323 |
- TimepointMonths = dplyr::if_else( |
|
324 |
- condition = is.na(.data$TimepointMonths), |
|
325 |
- false = .data$TimepointMonths, |
|
326 |
- true = dplyr::if_else( |
|
327 |
- condition = as.numeric(.data$TimePoint) == 0, |
|
328 |
- true = 0, |
|
329 |
- false = dplyr::if_else( |
|
330 |
- condition = as.numeric(.data$TimePoint) > 0 & |
|
331 |
- as.numeric(.data$TimePoint) < 30, |
|
332 |
- true = ceiling(as.numeric(.data$TimePoint) / 30), |
|
333 |
- false = round(as.numeric(.data$TimePoint) / 30) |
|
334 |
- ) |
|
335 |
- ) |
|
336 |
- ), |
|
337 |
- TimepointYears = dplyr::if_else( |
|
338 |
- condition = is.na(.data$TimepointYears), |
|
339 |
- false = .data$TimepointYears, |
|
340 |
- true = dplyr::if_else( |
|
341 |
- condition = as.numeric(.data$TimePoint) == 0, |
|
342 |
- true = 0, |
|
343 |
- false = dplyr::if_else( |
|
344 |
- condition = as.numeric(.data$TimePoint) > 0 & |
|
345 |
- as.numeric(.data$TimePoint) < 360, |
|
346 |
- true = ceiling(as.numeric(.data$TimePoint) / 360), |
|
347 |
- false = round(as.numeric(.data$TimePoint) / 360) |
|
324 |
+ dplyr::mutate( |
|
325 |
+ TimepointMonths = dplyr::if_else( |
|
326 |
+ condition = as.numeric(.data$TimePoint) == 0, |
|
327 |
+ true = 0, |
|
328 |
+ false = dplyr::if_else( |
|
329 |
+ condition = as.numeric(.data$TimePoint) > 0 & |
|
330 |
+ as.numeric(.data$TimePoint) < 30, |
|
331 |
+ true = ceiling(as.numeric(.data$TimePoint) / 30), |
|
332 |
+ false = round(as.numeric(.data$TimePoint) / 30) |
|
333 |
+ ) |
|
334 |
+ ), |
|
335 |
+ TimepointYears = dplyr::if_else( |
|
336 |
+ condition = as.numeric(.data$TimePoint) == 0, |
|
337 |
+ true = 0, |
|
338 |
+ false = ceiling(as.numeric(.data$TimePoint) / 360) |
|
348 | 339 |
) |
349 |
- ) |
|
340 |
+ ) %>% |
|
341 |
+ dplyr::mutate( |
|
342 |
+ TimepointMonths = stringr::str_pad( |
|
343 |
+ as.character(.data$TimepointMonths), |
|
344 |
+ pad = "0", side = "left", width = 2 |
|
345 |
+ ), |
|
346 |
+ TimepointYears = stringr::str_pad( |
|
347 |
+ as.character(.data$TimepointYears), |
|
348 |
+ pad = "0", side = "left", width = 2 |
|
349 |
+ ), |
|
350 | 350 |
) |
351 |
- ) %>% |
|
352 |
- dplyr::mutate( |
|
353 |
- TimepointMonths = stringr::str_pad( |
|
354 |
- as.character(.data$TimepointMonths), |
|
355 |
- pad = "0", side = "left", width = 2 |
|
356 |
- ), |
|
357 |
- TimepointYears = stringr::str_pad( |
|
358 |
- as.character(.data$TimepointYears), |
|
359 |
- pad = "0", side = "left", width = 2 |
|
360 |
- ), |
|
361 |
- ) |
|
351 |
+ } |
|
352 |
+ |
|
362 | 353 |
widget <- if (something_to_report) { |
363 | 354 |
summary_report <- .summary_af_import_msg( |
364 | 355 |
pars_prob = parsing_problems, dates_prob = date_problems, |
... | ... |
@@ -95,9 +95,16 @@ generate_Vispa2_launch_AF <- function(association_file, project, pool, path) { |
95 | 95 |
} |
96 | 96 |
files <- purrr::map2(project, pool, function(x, y) { |
97 | 97 |
selected_cols <- association_file %>% |
98 |
- dplyr::select(dplyr::all_of(reduced_AF_columns())) %>% |
|
98 |
+ dplyr::select(dplyr::all_of(reduced_AF_columns()), |
|
99 |
+ .data$concatenatePoolIDSeqRun) %>% |
|
99 | 100 |
dplyr::filter(.data$ProjectID == x, .data$PoolID == y) %>% |
100 |
- dplyr::mutate(TagID2 = .data$TagID, .before = .data$TagID) |
|
101 |
+ dplyr::mutate(TagID2 = .data$TagID, .before = .data$TagID) %>% |
|
102 |
+ dplyr::mutate(PoolName = dplyr::if_else( |
|
103 |
+ !is.na(.data$concatenatePoolIDSeqRun), |
|
104 |
+ .data$concatenatePoolIDSeqRun, |
|
105 |
+ .data$PoolID |
|
106 |
+ )) %>% |
|
107 |
+ dplyr::select(-.data$PoolID, -.data$concatenatePoolIDSeqRun) |
|
101 | 108 |
}) %>% purrr::set_names(paste0(project, "-", pool, "_AF.tsv")) |
102 | 109 |
purrr::walk2(files, names(files), function(x, y) { |
103 | 110 |
complete_path <- fs::path(path, y) |