lint R file

tools/plot_ragtag_paf/plot_ragtag_paf.R

@@ -1,11 +1,11 @@
 #!/usr/bin/env Rscript
 
 options(
-  show.error.messages = F,
-  error = function() {
-    cat(geterrmessage(), file = stderr())
-    q("no", 1, F)
-  }
+    show.error.messages = F,
+    error = function() {
+        cat(geterrmessage(), file = stderr())
+        q("no", 1, F)
+    }
 )
 
 library(data.table)
@@ -23,70 +23,70 @@ args <- commandArgs(trailingOnly = TRUE)
 
 # Adjust the PAF coordinates to the continuous x-axis
 adjust_coords <- function(qname, qstart, qend, tname, tstart, tend) {
-  my_qstart <- lookup_qstart(qname)
-  my_tstart <- lookup_tstart(tname)
-  return(
-    data.table(
-      adj_qstart = qstart + my_qstart,
-      adj_qend = qend + my_qstart,
-      adj_tstart = tstart + my_tstart,
-      adj_tend = tend + my_tstart
+    my_qstart <- lookup_qstart(qname)
+    my_tstart <- lookup_tstart(tname)
+    return(
+        data.table(
+            adj_qstart = qstart + my_qstart,
+            adj_qend = qend + my_qstart,
+            adj_tstart = tstart + my_tstart,
+            adj_tend = tend + my_tstart
+        )
     )
-  )
 }
 
 # calculate spacing between contigs so the ref and query take up the same x-axis
 # space
 get_padding <- function(paf) {
-  tlen_sum <- unique(paf, by = "tname")[, sum(tlen)]
-  tgaps_total <- paf[, length(unique(tname))]
-
-  qlen_sum <- unique(paf, by = "qname")[, sum(qlen)]
-  qgaps_total <- paf[, length(unique(qname))]
-
-  # the minumum gap is going to be one tenth of the x-axis space
-  if (tlen_sum > qlen_sum) {
-    min_gap <- (tlen_sum * gap_size) / tgaps_total
-    full_tlen <- tlen_sum + (tgaps_total * min_gap)
-
-    total_qpadding <- full_tlen - qlen_sum
-    return(
-      c(
-        "t_padding" = min_gap,
-        "q_padding" = total_qpadding / qgaps_total
-      )
-    )
-  } else if (tlen_sum < qlen_sum) {
-    min_gap <- (qlen_sum * gap_size) / qgaps_total
-    full_qlen <- qlen_sum + (qgaps_total * min_gap)
-
-    total_tpadding <- full_qlen - tlen_sum
-
-    return(
-      c(
-        "t_padding" = total_tpadding / tgaps_total,
-        "q_padding" = min_gap
-      )
-    )
-  } else {
-    min_gap <- (tlen_sum * gap_size) / tgaps_total
-    return(
-      c(
-        "t_padding" = min_gap,
-        "q_padding" = min_gap
-      )
-    )
-  }
+    tlen_sum <- unique(paf, by = "tname")[, sum(tlen)]
+    tgaps_total <- paf[, length(unique(tname))]
+
+    qlen_sum <- unique(paf, by = "qname")[, sum(qlen)]
+    qgaps_total <- paf[, length(unique(qname))]
+
+    # the minumum gap is going to be one tenth of the x-axis space
+    if (tlen_sum > qlen_sum) {
+        min_gap <- (tlen_sum * gap_size) / tgaps_total
+        full_tlen <- tlen_sum + (tgaps_total * min_gap)
+
+        total_qpadding <- full_tlen - qlen_sum
+        return(
+            c(
+                "t_padding" = min_gap,
+                "q_padding" = total_qpadding / qgaps_total
+            )
+        )
+    } else if (tlen_sum < qlen_sum) {
+        min_gap <- (qlen_sum * gap_size) / qgaps_total
+        full_qlen <- qlen_sum + (qgaps_total * min_gap)
+
+        total_tpadding <- full_qlen - tlen_sum
+
+        return(
+            c(
+                "t_padding" = total_tpadding / tgaps_total,
+                "q_padding" = min_gap
+            )
+        )
+    } else {
+        min_gap <- (tlen_sum * gap_size) / tgaps_total
+        return(
+            c(
+                "t_padding" = min_gap,
+                "q_padding" = min_gap
+            )
+        )
+    }
 }
 
 # offsets for the adjusted coordinates
 lookup_tstart <- function(x) {
-  return(unique(tstarts[tname == x, shift_tstart]))
+    return(unique(tstarts[tname == x, shift_tstart]))
 }
 
 
 lookup_qstart <- function(x) {
-  return(unique(qstarts[qname == x, shift_qstart]))
+    return(unique(qstarts[qname == x, shift_qstart]))
 }
 
 
@@ -145,30 +145,30 @@ qstarts <- unique(qpaf[, .(qname, shift_qstart)])
 
 # adjust the alignment coordinates
 paf_dt[,
-  c(
-    "adj_qstart",
-    "adj_qend",
-    "adj_tstart",
-    "adj_tend"
-  ) := adjust_coords(qname, qstart, qend, tname, tstart, tend),
-  by = .(qname, qstart, qend, tname, tstart, tend)
+    c(
+        "adj_qstart",
+        "adj_qend",
+        "adj_tstart",
+        "adj_tend"
+    ) := adjust_coords(qname, qstart, qend, tname, tstart, tend),
+    by = .(qname, qstart, qend, tname, tstart, tend)
 ]
 
 # generate polygons. P is for primary alignments only
 polygon_y_bump <- 0.017 # account for contig thickness
 paf_polygons <- paf_dt[
-  tp == "P" & nmatch >= min_nmatch,
-  .(
-    x = c(adj_tstart, adj_qstart, adj_qend, adj_tend),
-    y = c(
-      t_y + polygon_y_bump,
-      q_y - polygon_y_bump,
-      q_y - polygon_y_bump,
-      t_y + polygon_y_bump
+    tp == "P" & nmatch >= min_nmatch,
+    .(
+        x = c(adj_tstart, adj_qstart, adj_qend, adj_tend),
+        y = c(
+            t_y + polygon_y_bump,
+            q_y - polygon_y_bump,
+            q_y - polygon_y_bump,
+            t_y + polygon_y_bump
+        ),
+        id = paste0("polygon", .GRP)
     ),
-    id = paste0("polygon", .GRP)
-  ),
-  by = .(qname, qstart, qend, tname, tstart, tend)
+    by = .(qname, qstart, qend, tname, tstart, tend)
 ]
 
 # set up plot
@@ -180,78 +180,78 @@ middle_x <- tpaf[1, shift_tstart] + tpaf[.N, pad_tend] / 2
 
 all_contig_names <- c(tpaf[, unique(tname)])
 all_colours <- viridis(
-  length(all_contig_names) + palette_space + 1
+    length(all_contig_names) + palette_space + 1
 )
 names(all_colours) <- c(
-  "query",
-  rep("blank", palette_space),
-  all_contig_names
+    "query",
+    rep("blank", palette_space),
+    all_contig_names
 )
 
 # Plot the ideogram with ribbons connecting the two sets of contigs
 gp <- ggplot() +
-  theme_void(base_family = "Lato", base_size = 12) +
-  scale_fill_manual(
-    values = all_colours, guide = "none"
-  ) +
-  scale_colour_manual(
-    values = all_colours, guide = "none"
-  ) +
-  geom_polygon(
-    data = paf_polygons,
-    aes(
-      x = x, y = y, group = id, fill = tname
-    ), alpha = 0.5
-  ) +
-  geom_segment(
-    data = tpaf,
-    aes(
-      x = shift_tstart,
-      xend = pad_tend,
-      colour = tname
-    ),
-    y = t_y,
-    linewidth = 5,
-    lineend = "butt"
-  ) +
-  geom_segment(
-    data = qpaf,
-    aes(
-      x = shift_qstart,
-      xend = pad_qend
-    ),
-    colour = all_colours[["query"]],
-    y = q_y,
-    linewidth = 5,
-    lineend = "butt"
-  ) +
-  ylim(
-    t_y - y_axis_space,
-    q_y + y_axis_space
-  ) +
-  annotate(
-    geom = "text",
-    label = "Query contigs",
-    x = middle_x,
-    y = q_y + (y_axis_space / 3),
-    hjust = 0.5,
-    vjust = 0.5
-  ) +
-  annotate(
-    geom = "text",
-    label = "Reference contigs",
-    x = middle_x,
-    y = t_y - (y_axis_space / 3),
-    hjust = 0.5,
-    vjust = 0.5
-  )
+    theme_void(base_family = "Lato", base_size = 12) +
+    scale_fill_manual(
+        values = all_colours, guide = "none"
+    ) +
+    scale_colour_manual(
+        values = all_colours, guide = "none"
+    ) +
+    geom_polygon(
+        data = paf_polygons,
+        aes(
+            x = x, y = y, group = id, fill = tname
+        ), alpha = 0.5
+    ) +
+    geom_segment(
+        data = tpaf,
+        aes(
+            x = shift_tstart,
+            xend = pad_tend,
+            colour = tname
+        ),
+        y = t_y,
+        linewidth = 5,
+        lineend = "butt"
+    ) +
+    geom_segment(
+        data = qpaf,
+        aes(
+            x = shift_qstart,
+            xend = pad_qend
+        ),
+        colour = all_colours[["query"]],
+        y = q_y,
+        linewidth = 5,
+        lineend = "butt"
+    ) +
+    ylim(
+        t_y - y_axis_space,
+        q_y + y_axis_space
+    ) +
+    annotate(
+        geom = "text",
+        label = "Query contigs",
+        x = middle_x,
+        y = q_y + (y_axis_space / 3),
+        hjust = 0.5,
+        vjust = 0.5
+    ) +
+    annotate(
+        geom = "text",
+        label = "Reference contigs",
+        x = middle_x,
+        y = t_y - (y_axis_space / 3),
+        hjust = 0.5,
+        vjust = 0.5
+    )
 
 ggsave(plot_file,
-  gp,
-  width = plot_width,
-  height = plot_height,
-  units = "mm",
-  device = cairo_pdf
+    gp,
+    width = plot_width,
+    height = plot_height,
+    units = "mm",
+    device = cairo_pdf
 )
 
 sessionInfo()