feat: formatted all R code with 'styler'

showteeth · Apr 29, 2024 · c2a2001 · c2a2001
1 parent a156490
commit c2a2001
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Showing 27 changed files with 476 additions and 340 deletions.
diff --git a/R/ConsensusPeak.R b/R/ConsensusPeak.R
@@ -26,7 +26,6 @@
 GetConsensusPeak <- function(peak.file, peak.folder = NULL, mspc.path = NULL, rep.type = c("bio", "tec"), stringency.threshold = 1e-8,
                              weak.threshold = 1e-4, gamma = 1e-8, alpha = 0.05, min.overlap.num = 1,
                              multiple.intersections = c("Lowest", "Highest"), parallelism.degree = 1) {
-
   # check parameters
   rep.type <- match.arg(arg = rep.type)
   multiple.intersections <- match.arg(arg = multiple.intersections)

diff --git a/R/LoadTrack.R b/R/LoadTrack.R
@@ -56,17 +56,16 @@
 #'   meta.info = sample.meta
 #' )
 LoadTrackFile <- function(
-  track.file, track.folder = NULL,
-  format = c("bam", "wig", "bw", "bedgraph", "txt"),
-  region = NULL, extend = 2000,
-  gtf.gr = NULL, gene.name = "HNRNPC",
-  gene.name.type = c("gene_name", "gene_id"),
-  meta.info = NULL, meta.file = "",
-  bamcoverage.path = NULL,
-  norm.method = c("RPKM", "CPM", "BPM", "RPGC", "None"),
-  single.nuc = FALSE, single.nuc.region = NULL,
-  bin.size = 10, bc.extra.para = NULL, n.cores = 1
-) {
+    track.file, track.folder = NULL,
+    format = c("bam", "wig", "bw", "bedgraph", "txt"),
+    region = NULL, extend = 2000,
+    gtf.gr = NULL, gene.name = "HNRNPC",
+    gene.name.type = c("gene_name", "gene_id"),
+    meta.info = NULL, meta.file = "",
+    bamcoverage.path = NULL,
+    norm.method = c("RPKM", "CPM", "BPM", "RPGC", "None"),
+    single.nuc = FALSE, single.nuc.region = NULL,
+    bin.size = 10, bc.extra.para = NULL, n.cores = 1) {
   # check parameters
   format <- match.arg(arg = format)
   gene.name.type <- match.arg(arg = gene.name.type)
@@ -83,8 +82,8 @@ LoadTrackFile <- function(
     if (format == "bam") {
       seqnames <- Rsamtools::scanBamHeader(track.file[1]) %>%
         lapply(function(x) x$targets) %>%
-        unname %>%
-        unlist
+        unname() %>%
+        unlist()
       gr <- GenomicRanges::GRanges(
         seqnames = names(seqnames[1]),
         IRanges(start = 1, end = min(100000, seqnames[1]))
@@ -128,20 +127,20 @@ LoadTrackFile <- function(
       BiocParallel::bplapply(track.file, BPPARAM = BiocParallel::MulticoreParam(), FUN = index_bam)
     }
     if (single.nuc) {
-        if (is.null(n.cores) || n.cores == 1) {
-          track.list <- lapply(
-            track.file,
-            single_nuc_cov,
-            single.nuc.region
-          )
-        } else {
-          track.list <- BiocParallel::bplapply(
-            track.file,
-            BPPARAM = BiocParallel::MulticoreParam(),
-            FUN = single_nuc_cov,
-            single.nuc.region
-          )
-        }
+      if (is.null(n.cores) || n.cores == 1) {
+        track.list <- lapply(
+          track.file,
+          single_nuc_cov,
+          single.nuc.region
+        )
+      } else {
+        track.list <- BiocParallel::bplapply(
+          track.file,
+          BPPARAM = BiocParallel::MulticoreParam(),
+          FUN = single_nuc_cov,
+          single.nuc.region
+        )
+      }
     } else {
       if (norm.method == "None") {
         message("Calculating coverage with GenomicAlignments when 'norm.method = None'")
@@ -310,8 +309,7 @@ single_nuc_cov <- function(x, single.nuc.region) {
 }
 
 bam_coverage <- function(
-  x, bamcoverage.path, bin.size, norm.method, bc.extra.para, gr
-) {
+    x, bamcoverage.path, bin.size, norm.method, bc.extra.para, gr) {
   # bigwig file
   out.bw.file <- tempfile(fileext = c(".bw"))
   # prepare bamCoverage cmd

diff --git a/R/geom_base.R b/R/geom_base.R
@@ -76,8 +76,10 @@
 #'   single.nuc = TRUE,
 #'   rect.color = "white"
 #' ) +
-#'   geom_base(bam.file = bam.file,
-#'             bs.fa.seq = BSgenome.Hsapiens.UCSC.hg19)
+#'   geom_base(
+#'     bam.file = bam.file,
+#'     bs.fa.seq = BSgenome.Hsapiens.UCSC.hg19
+#'   )
 #'
 geom_base <- function(bam.file, fa.file = NULL, bs.fa.seq = NULL, chr.split = "[[:space:]]",
                       nuc.offset = -0.1, nuc.size = 4, nuc.padding = 0.05, nuc.padding.r = 0,
@@ -93,16 +95,17 @@ geom_base <- function(bam.file, fa.file = NULL, bs.fa.seq = NULL, chr.split = "[
                         "*" = "#FFC0CB"
                       ), aa.border.color = "white", aa.size = 4, aa.margin = 2, aa.height = 0.4,
                       plot.space = 2.5, plot.height = 0.5) {
-  structure(list(
-    bam.file = bam.file, fa.file = fa.file, bs.fa.seq = bs.fa.seq, chr.split = chr.split,
-    nuc.offset = nuc.offset, nuc.size = nuc.size, nuc.padding = nuc.padding, nuc.padding.r = nuc.padding.r,
-    nuc.color = nuc.color, guide.line = guide.line, guide.line.color = guide.line.color, guide.line.type = guide.line.type,
-    mark.type = mark.type, star.size = star.size,
-    show.aa = show.aa, sens = sens, numcode = numcode, NAstring = NAstring, ambiguous = ambiguous,
-    aa.color = aa.color, aa.border.color = aa.border.color, aa.size = aa.size, aa.margin = aa.margin, aa.height = aa.height,
-    plot.space = plot.space, plot.height = plot.height
-  ),
-  class = "base"
+  structure(
+    list(
+      bam.file = bam.file, fa.file = fa.file, bs.fa.seq = bs.fa.seq, chr.split = chr.split,
+      nuc.offset = nuc.offset, nuc.size = nuc.size, nuc.padding = nuc.padding, nuc.padding.r = nuc.padding.r,
+      nuc.color = nuc.color, guide.line = guide.line, guide.line.color = guide.line.color, guide.line.type = guide.line.type,
+      mark.type = mark.type, star.size = star.size,
+      show.aa = show.aa, sens = sens, numcode = numcode, NAstring = NAstring, ambiguous = ambiguous,
+      aa.color = aa.color, aa.border.color = aa.border.color, aa.size = aa.size, aa.margin = aa.margin, aa.height = aa.height,
+      plot.space = plot.space, plot.height = plot.height
+    ),
+    class = "base"
   )
 }
 
@@ -122,8 +125,10 @@ ggplot_add.base <- function(object, plot, object_name) {
   # plot.region.end <- plot.data[nrow(plot.data), "start"]
   plot.region.end <- max(plot.data[, "start"])
   region <-
-    GenomicRanges::GRanges(plot.chr,
-                           IRanges::IRanges(plot.region.start, plot.region.end))
+    GenomicRanges::GRanges(
+      plot.chr,
+      IRanges::IRanges(plot.region.start, plot.region.end)
+    )
 
   # get parameters
   bam.file <- object$bam.file
@@ -155,9 +160,11 @@ ggplot_add.base <- function(object, plot, object_name) {
 
   # get position AGCT frequency
   pos.nuc.freq <-
-    GenomicAlignments::alphabetFrequencyFromBam(bam.file,
-                                                param = region,
-                                                baseOnly = TRUE)
+    GenomicAlignments::alphabetFrequencyFromBam(
+      bam.file,
+      param = region,
+      baseOnly = TRUE
+    )
   # filter out others
   pos.nuc.freq <-
     pos.nuc.freq[, c("A", "G", "C", "T")] %>% as.data.frame()
@@ -202,15 +209,15 @@ ggplot_add.base <- function(object, plot, object_name) {
   # get position with alt
   alt.pos <- pos.nuc.freq.long %>%
     dplyr::filter(.data$Ref == .data$Base &
-                    .data$Total != .data$Freq) %>%
+      .data$Total != .data$Freq) %>%
     dplyr::pull(.data$Pos) %>%
     unique()
   alt.pos.nuc.freq.long <-
     pos.nuc.freq.long %>% dplyr::filter(.data$Pos %in% c(alt.pos))
   # get position without alt
   ref.pos <- pos.nuc.freq.long %>%
     dplyr::filter(.data$Ref == .data$Base &
-                    .data$Total == .data$Freq) %>%
+      .data$Total == .data$Freq) %>%
     dplyr::pull(.data$Pos) %>%
     unique()
   ref.pos.nuc.freq.long <-
@@ -336,9 +343,11 @@ ggplot_add.base <- function(object, plot, object_name) {
         label.r = unit(nuc.padding.r, "lines")
       ) +
       labs(y = "Base") +
-      geom_hline(yintercept = guide.line,
-                 color = guide.line.color,
-                 linetype = guide.line.type)
+      geom_hline(
+        yintercept = guide.line,
+        color = guide.line.color,
+        linetype = guide.line.type
+      )
 
     # make final AA plot
     options(digits = nchar(max(list_translated[[1]]$Pos)) + 1)
@@ -358,17 +367,20 @@ ggplot_add.base <- function(object, plot, object_name) {
           ),
           color = aa.border.color
         ) +
-        geom_text(data = list_translated[[reading_frame]],
-                  aes_string(x = "Pos", y = "y", label = "anno"))
+        geom_text(
+          data = list_translated[[reading_frame]],
+          aes_string(x = "Pos", y = "y", label = "anno")
+        )
     }
     aa_plot <- aa_plot +
       labs(y = "AA") +
       theme_aa(margin.len = aa.margin, fill.color = aa.color)
     final.plot <-
       patchwork::wrap_plots(base.plot,
-                            aa_plot,
-                            ncol = 1,
-                            heights = c(1, aa.height))
+        aa_plot,
+        ncol = 1,
+        heights = c(1, aa.height)
+      )
   } else {
     # create plot without amino acid
     final.plot <- base.plot +
@@ -387,9 +399,11 @@ ggplot_add.base <- function(object, plot, object_name) {
         label.r = unit(nuc.padding.r, "lines")
       ) +
       labs(y = "Base") +
-      geom_hline(yintercept = guide.line,
-                 color = guide.line.color,
-                 linetype = guide.line.type)
+      geom_hline(
+        yintercept = guide.line,
+        color = guide.line.color,
+        linetype = guide.line.type
+      )
   }
 
   # assemble plot

diff --git a/R/geom_cnv.R b/R/geom_cnv.R
@@ -42,12 +42,13 @@
 geom_cnv <- function(cnv.df, bin.col = 3, cn.col = 4, ref.cn = 2,
                      bin.point.color = "grey", bin.point.alpha = 0.6, cn.line.color = "red",
                      ref.line.color = "black", plot.space = 0.1, plot.height = 0.2) {
-  structure(list(
-    cnv.df = cnv.df, bin.col = bin.col, cn.col = cn.col, ref.cn = ref.cn,
-    bin.point.color = bin.point.color, bin.point.alpha = bin.point.alpha, cn.line.color = cn.line.color,
-    ref.line.color = ref.line.color, plot.space = plot.space, plot.height = plot.height
-  ),
-  class = "cnv"
+  structure(
+    list(
+      cnv.df = cnv.df, bin.col = bin.col, cn.col = cn.col, ref.cn = ref.cn,
+      bin.point.color = bin.point.color, bin.point.alpha = bin.point.alpha, cn.line.color = cn.line.color,
+      ref.line.color = ref.line.color, plot.space = plot.space, plot.height = plot.height
+    ),
+    class = "cnv"
   )
 }
 

diff --git a/R/geom_coverage.R b/R/geom_coverage.R
@@ -88,9 +88,10 @@
 #'   geom_coverage(
 #'     data = track.df, facet.key = "Type",
 #'     mark.region = data.frame(
-#'       start = c(21678900,21732001,21737590),
-#'       end = c(21679900,21732400,21737650),
-#'       label=c("M1", "M2", "M3")),
+#'       start = c(21678900, 21732001, 21737590),
+#'       end = c(21679900, 21732400, 21737650),
+#'       label = c("M1", "M2", "M3")
+#'     ),
 #'     mark.color = grey(0.4)
 #'   )
 #'
@@ -112,7 +113,8 @@ geom_coverage <- function(data, mapping = NULL, color = NULL, rect.color = NA,
       if (!is.null(color)) {
         testcolors <- sapply(color, function(x) {
           tryCatch(is.matrix(col2rgb(x)),
-                   error = function(e) FALSE)
+            error = function(e) FALSE
+          )
         })
         if (length(color) < length(unique(data[, group.key]))) {
           warning("Fewer colors provided than there are groups in ", group.key, " variable, falling back to default colors")
@@ -259,9 +261,10 @@ geom_coverage <- function(data, mapping = NULL, color = NULL, rect.color = NA,
 
     if (range.position == "in") {
       data.range <- data.range %>%
-        dplyr::summarise(.groups = "drop_last",
-                         min_score = pretty(.data[[ymax.str]])[1],
-                         max_score = tail(pretty(.data[[ymax.str]]), 1)
+        dplyr::summarise(
+          .groups = "drop_last",
+          min_score = pretty(.data[[ymax.str]])[1],
+          max_score = tail(pretty(.data[[ymax.str]]), 1)
         )
       data.range$label <- paste0("[", data.range$min_score, ", ", data.range$max_score, "]")
       region.range <- geom_text(

diff --git a/R/geom_feature.R b/R/geom_feature.R
@@ -42,11 +42,12 @@
 #' #   )
 geom_feature <- function(feature.file = NULL, feature.df = NULL, feature.color = "black", feature.size = 5,
                          plot.space = 0.1, plot.height = 0.1) {
-  structure(list(
-    feature.file = feature.file, feature.df = feature.df, feature.color = feature.color, feature.size = feature.size,
-    plot.space = plot.space, plot.height = plot.height
-  ),
-  class = "feature"
+  structure(
+    list(
+      feature.file = feature.file, feature.df = feature.df, feature.color = feature.color, feature.size = feature.size,
+      plot.space = plot.space, plot.height = plot.height
+    ),
+    class = "feature"
   )
 }
 

diff --git a/R/geom_gc.R b/R/geom_gc.R
@@ -37,12 +37,13 @@
 geom_gc <- function(fa.file = NULL, bs.fa.seq = NULL, chr.split = "[[:space:]]", guide.line = NULL,
                     line.color = "black", guide.line.color = "red", guide.line.type = "dashed",
                     plot.space = 0.1, plot.height = 0.2) {
-  structure(list(
-    fa.file = fa.file, bs.fa.seq = bs.fa.seq, chr.split = chr.split, guide.line = guide.line,
-    line.color = line.color, guide.line.color = guide.line.color, guide.line.type = guide.line.type,
-    plot.space = plot.space, plot.height = plot.height
-  ),
-  class = "gc"
+  structure(
+    list(
+      fa.file = fa.file, bs.fa.seq = bs.fa.seq, chr.split = chr.split, guide.line = guide.line,
+      line.color = line.color, guide.line.color = guide.line.color, guide.line.type = guide.line.type,
+      plot.space = plot.space, plot.height = plot.height
+    ),
+    class = "gc"
   )
 }
 

diff --git a/R/geom_gene.R b/R/geom_gene.R
@@ -71,8 +71,10 @@ geom_gene <- function(gtf.gr,
                       arrow.gap = NULL,
                       arrow.num = 50,
                       color.by = "strand",
-                      fill.color = c("-" = "cornflowerblue",
-                                     "+" = "darkolivegreen3"),
+                      fill.color = c(
+                        "-" = "cornflowerblue",
+                        "+" = "darkolivegreen3"
+                      ),
                       show.utr = FALSE,
                       label.size = 3,
                       label.vjust = 2,

diff --git a/R/geom_ideogram.R b/R/geom_ideogram.R
@@ -78,18 +78,18 @@ geom_ideogram <- function(genome = "hg19", mark.color = "red", mark.alpha = 0.7,
                           highlight.centromere = FALSE, highlight.color = "green", highlight.alpha = 0.7, highlight.line.size = 1,
                           highlight.shadow.color = "black", highlight.shadow.alpha = 0.7, highlight.shadow.line.size = 1,
                           plot.space = 0.1, plot.height = 0.1) {
-
   # test if suggested package is installed
   requireNamespace("ggbio", quietly = TRUE)
 
-  structure(list(
-    genome = genome, mark.color = mark.color, mark.alpha = mark.alpha, mark.line.size = mark.line.size,
-    add.shadow = add.shadow, shadow.color = shadow.color, shadow.alpha = shadow.alpha, shadow.line.size = shadow.line.size,
-    highlight.centromere = highlight.centromere, highlight.color = highlight.color, highlight.alpha = highlight.alpha,
-    highlight.line.size = highlight.line.size, highlight.shadow.color = highlight.shadow.color, highlight.shadow.alpha = highlight.shadow.alpha,
-    highlight.shadow.line.size = highlight.shadow.line.size, plot.space = plot.space, plot.height = plot.height
-  ),
-  class = "ideogram"
+  structure(
+    list(
+      genome = genome, mark.color = mark.color, mark.alpha = mark.alpha, mark.line.size = mark.line.size,
+      add.shadow = add.shadow, shadow.color = shadow.color, shadow.alpha = shadow.alpha, shadow.line.size = shadow.line.size,
+      highlight.centromere = highlight.centromere, highlight.color = highlight.color, highlight.alpha = highlight.alpha,
+      highlight.line.size = highlight.line.size, highlight.shadow.color = highlight.shadow.color, highlight.shadow.alpha = highlight.shadow.alpha,
+      highlight.shadow.line.size = highlight.shadow.line.size, plot.space = plot.space, plot.height = plot.height
+    ),
+    class = "ideogram"
   )
 }