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Update plotNovel function to use integer x-axis labels and adjust limits #47

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Merged
ssnn-airr merged 1 commit into from
Apr 13, 2026
Merged

Update plotNovel function to use integer x-axis labels and adjust limits #47

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2 changes: 1 addition & 1 deletion DESCRIPTION
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
Package: tigger
Type: Package
Version: 1.1.2.999
Date: 2026-04-01
Date: 2026-04-13
Authors@R: c(person("Daniel", "Gadala-Maria", role=c("aut"),
email="daniel.gadala-maria@yale.edu"),
person("Susanna", "Marquez", role=c("aut", "cre"),
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8 changes: 8 additions & 0 deletions R/functions.R
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Expand Up @@ -832,6 +832,10 @@ plotNovel <- function(data, novel_row, v_call="v_call", j_call="j_call",
factor(levels = names(DNA_COLORS))
pos_muts$GERMLINE <- names(germline)

x_range <- range(pos_muts$MUT_COUNT)
x_limits <- c(x_range[1] - 0.5, x_range[2] + 0.5)
x_breaks <- seq(x_range[1], x_range[2], by = 1)

# MAKE THE FIRST PLOT
if (!is.na(novel_imgt)) {
POLYCOLORS <- setNames(DNA_COLORS[c(4,3)], c("False", "True")) # blue #3C88EE, red #EB413C
Expand All @@ -844,6 +848,7 @@ plotNovel <- function(data, novel_row, v_call="v_call", j_call="j_call",
geom_line(data=filter(pos_muts, !!rlang::sym("Polymorphic") == "True"), linewidth=0.75) +
facet_grid(GERMLINE ~ .) +
scale_color_manual(values = POLYCOLORS) +
scale_x_continuous(limits = x_limits, breaks = x_breaks) +
ylim(0,1) +
xlab("Mutation Count (Sequence)") +
ylab("Mutation Frequency (Position)") +
Expand All @@ -861,6 +866,7 @@ plotNovel <- function(data, novel_row, v_call="v_call", j_call="j_call",
geom_line(linewidth=0.75) +
facet_grid(GERMLINE ~ .) +
scale_color_manual(values=POLYCOLORS) +
scale_x_continuous(limits = x_limits, breaks = x_breaks) +
ylim(0, 1) +
xlab("Mutation Count (Sequence)") +
ylab("Mutation Frequency (Position)") +
Expand All @@ -887,6 +893,7 @@ plotNovel <- function(data, novel_row, v_call="v_call", j_call="j_call",
guides(fill = guide_legend("Nucleotide", ncol=4)) +
xlab("Mutation Count (Sequence)") +
ylab("Sequence Count") +
scale_x_continuous(limits = x_limits, breaks = x_breaks) +
scale_fill_manual(values=DNA_COLORS, breaks=names(DNA_COLORS),
drop=FALSE) +
theme_bw() +
Expand All @@ -899,6 +906,7 @@ plotNovel <- function(data, novel_row, v_call="v_call", j_call="j_call",
p2 <- ggplot(p2_data, aes(x=!!rlang::sym("MUT_COUNT"))) +
geom_bar(width=0.9) +
xlab("Mutation Count (Sequence)") + ylab("Sequence Count") +
scale_x_continuous(limits = x_limits, breaks = x_breaks) +
theme_bw() +
theme(legend.position=c(1,1), legend.justification=c(1,1),
legend.background=element_rect(fill = "transparent"))
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