biopipen 0.21.0__py3-none-any.whl → 0.34.26__py3-none-any.whl

biopipen/utils/single_cell.R

@@ -1,115 +0,0 @@
-suppressPackageStartupMessages(library(rlang))
-suppressPackageStartupMessages(library(dplyr))
-suppressPackageStartupMessages(library(tidyr))
-suppressPackageStartupMessages(library(immunarch))
-
-#' Expand a Immunarch object into cell-level
-#'
-#' Here is how the data is expanded:
-#' 1. Expand `$data` by Barcode (other columns are copied)
-#' 2. Add sample to `Sample` column
-#' 3. Add columns from `$meta`
-#'
-#' @param immdata Immunarch object
-#' @return A data frame
-#'
-#' @example
-#' immunarch::immdata$data$MS1 |> head()
-#' #   Clones Proportion CDR3.nt            CDR3.aa V.name D.name J.name V.end D.start D.end J.start VJ.ins VD.ins DJ.ins Sequence
-#' #    <dbl>      <dbl> <chr>              <chr>   <chr>  <chr>  <chr>  <int>   <int> <int>   <int>  <dbl>  <dbl>  <dbl> <lgl>
-#' # 1    539    0.0634  TGTGCCAGCAGCTTACA… CASSLQ… TRBV7… TRBD2  TRBJ2…    14      18    26      29     -1      3      2 NA
-#' # 2    320    0.0376  TGTGCCAGCAGCGTGTA… CASSVY… TRBV9  TRBD1  TRBJ2…    13      20    22      29     -1      6      6 NA
-#' immunarch::immdata$meta |> head()
-#' #   Sample  ID    Sex     Age Status Lane
-#' #   <chr>   <chr> <chr> <dbl> <chr>  <chr>
-#' # 1 A2-i129 C1    M        11 C      A
-#' # 2 A2-i131 C2    M         9 C      A
-#' # 3 A2-i133 C4    M        16 C      A
-#' # 4 A2-i132 C3    F         6 C      A
-#' # 5 A4-i191 C8    F        22 C      B
-#' # 6 A4-i192 C9    F        24 C      B
-#'
-#' @export
-expand_immdata <- function(immdata, cell_id = "Barcode") {
-    if (!cell_id %in% colnames(immdata$data[[1]])) {
-        stop(paste0("cell_id '", cell_id, "' not found in data"))
-    }
-    do.call(rbind, lapply(names(immdata$data), function(name) {
-        # Split barcodes
-        dat <- immdata$data[[name]] %>% separate_rows(!!sym(cell_id), sep = ";")
-        dat$Sample <- name
-        dat <- dat %>% left_join(immdata$meta, by = "Sample", suffix = c("_data", ""))
-
-        dat
-    }))
-}
-
-#' Filter expanded immdata
-#'
-#' @param exdata Expanded immdata
-#' @param filters Filters
-#' @return Filtered data
-#'
-#' @export
-filter_expanded_immdata <- function(exdata, filters, update_clones = FALSE) {
-    if (length(filters) == 0) {
-        return(exdata)
-    }
-    out <- exdata %>%
-        dplyr::filter(!!parse_expr(filters))
-    if (update_clones) {
-        out <- out %>%
-            group_by(Sample, CDR3.aa) %>%
-            mutate(Clones = n()) %>%
-            ungroup() %>%
-            group_by(Sample) %>%
-            mutate(Proportion = Clones / n()) %>%
-            ungroup() %>%
-            arrange(Sample, desc(Clones))
-    }
-    out
-}
-
-#' Convert expanded immdata to Immunarch object
-#'
-#' @param exdata Expanded immdata
-#' @param metacols Columns to be added to `$meta`
-#' @return Immunarch object
-#'
-#' @export
-immdata_from_expanded <- function(
-    exdata,
-    metacols = NULL,
-    cell_id = "Barcode",
-    update_clones = TRUE
-) {
-    if (is.null(metacols)) {
-        metacols = setdiff(colnames(exdata), c(
-            "Clones", "Proportion", "CDR3.nt", "CDR3.aa", "V.name", "D.name", "J.name",
-            "V.end", "D.start", "D.end", "J.start", "VJ.ins", "VD.ins", "DJ.ins",
-            "Sequence", "chain", "Barcode", "raw_clonotype_id", "ContigID", "C.name",
-            "CDR1.nt", "CDR2.nt", "CDR1.aa", "CDR2.aa", "FR1.nt", "FR2.nt", "FR3.nt",
-            "FR4.nt", "FR1.aa", "FR2.aa", "FR3.aa", "FR4.aa"
-        ))
-    }
-    out <- list(meta = exdata[, metacols, drop = FALSE])
-    out$meta <- out$meta[!duplicated(out$meta$Sample), , drop = FALSE]
-    out$data <- lapply(
-        split(
-            exdata[, setdiff(colnames(exdata), metacols), drop = FALSE],
-            exdata$Sample
-        ),
-        function(dat) {
-            ncells <- nrow(dat)
-            dat %>% group_by(CDR3.aa) %>%
-                summarise(
-                    Clones = ifelse(update_clones, n(), first(Clones)),
-                    Proportion = ifelse(update_clones, n() / ncells, first(Proportion)),
-                    !!sym(cell_id) := paste0(!!sym(cell_id), collapse = ";"),
-                    .groups = "drop"
-                ) %>%
-                arrange(desc(Clones))
-        }
-    )
-    out
-}

biopipen-0.21.0.dist-info/METADATA

@@ -1,22 +0,0 @@
-Metadata-Version: 2.1
-Name: biopipen
-Version: 0.21.0
-Summary: Bioinformatics processes/pipelines that can be run from `pipen run`
-License: MIT
-Author: pwwang
-Author-email: pwwang@pwwang.com
-Requires-Python: >=3.8,<4.0
-Classifier: License :: OSI Approved :: MIT License
-Classifier: Programming Language :: Python :: 3
-Classifier: Programming Language :: Python :: 3.8
-Classifier: Programming Language :: Python :: 3.9
-Classifier: Programming Language :: Python :: 3.10
-Classifier: Programming Language :: Python :: 3.11
-Classifier: Programming Language :: Python :: 3.12
-Provides-Extra: runinfo
-Requires-Dist: datar[pandas] (>=0.15.2,<0.16.0)
-Requires-Dist: pipen-board[report] (>=0.13,<0.14)
-Requires-Dist: pipen-cli-run (>=0.11,<0.12)
-Requires-Dist: pipen-filters (>=0.10,<0.11)
-Requires-Dist: pipen-runinfo (>=0.4,<0.5) ; extra == "runinfo"
-Requires-Dist: pipen-verbose (>=0.9,<0.10)

biopipen-0.21.0.dist-info/RECORD

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