1. NanoMethViz
  2. Commit f3668239db992a464dc03a7707fd17cdcd1e7bbc
Browse code

Added support for lower case modbam tags

shians authored on 09/10/2023 06:15:35
Showing 6 changed files
DESCRIPTION
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@@ -1,7 +1,7 @@
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 Package: NanoMethViz
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 Type: Package
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 Title: Visualise methlation data from Oxford Nanopore sequencing
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-Version: 2.7.8
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+Version: 2.7.9
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 Authors@R: c(
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     person("Shian", "Su", email = "[email protected]", role = c("cre", "aut")))
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 Description: NanoMethViz is a toolkit for visualising methylation data from
R/modbam.R
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@@ -103,31 +103,31 @@ read_bam <- function(bam_file, query = NULL) {
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             Rsamtools::ScanBamParam(
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                 flag = Rsamtools::scanBamFlag(isUnmappedQuery = FALSE),
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                 what = c("qname", "rname", "strand", "pos", "cigar", "seq"),
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-                tag = c("MM", "ML"),
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+                tag = c("MM", "ML", "Mm", "Ml"),
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                 which = query
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             )
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         } else {
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             Rsamtools::ScanBamParam(
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                 flag = Rsamtools::scanBamFlag(isUnmappedQuery = FALSE),
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                 what = c("qname", "rname", "strand", "pos", "cigar", "seq"),
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-                tag = c("MM", "ML")
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+                tag = c("MM", "ML", "Mm", "Ml")
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             )
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         }
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     }
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-    # determine_tag <- function(records) {
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-    #     if (is.null(records$tag$Mm) && is.null(records$tag$Ml)) {
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-    #         records$tag$Mm <- NULL
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-    #         records$tag$Ml <- NULL
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-    #     } else (is.null(records$tag$MM) && is.null(records$tag$ML)) {
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-    #         records$tag$MM <- records$tag$Mm
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-    #         records$tag$ML <- records$tag$Ml
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-    #         records$tag$Mm <- NULL
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-    #         records$tag$Ml <- NULL
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-    #     }
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-    #
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-    #     records
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-    # }
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+    determine_tag <- function(records) {
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+        if (is.null(records$tag$Mm) && is.null(records$tag$Ml)) {
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+            records$tag$Mm <- NULL
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+            records$tag$Ml <- NULL
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+        } else {
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+            records$tag$MM <- records$tag$Mm
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+            records$tag$ML <- records$tag$Ml
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+            records$tag$Mm <- NULL
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+            records$tag$Ml <- NULL
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+        }
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+
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+        records
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+    }
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     filter_modbam <- function(x) {
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         tag <- x$tag
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@@ -150,6 +150,7 @@ read_bam <- function(bam_file, query = NULL) {
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         bam_file,
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         param = modbam_param(query = query)
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     ) %>%
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+        map(determine_tag) %>%
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         map(filter_modbam)
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 }
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R/plot_gene_annotation.R
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@@ -81,7 +81,7 @@ plot_gene_annotation <- function(exons_df, plot_start, plot_end) {
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     .filter_regions <- function(exons_df, plot_start, plot_end) {
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         transcripts <- exons_df %>%
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             dplyr::summarise(
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-                .by = .data$transcript_id,
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+                .by = "transcript_id",
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                 start = min(.data$start),
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                 end = max(.data$end)
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             )
inst/peg3_lower_case.bam
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new file mode 100644
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Binary files /dev/null and b/inst/peg3_lower_case.bam differ
inst/peg3_lower_case.bam.bai
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new file mode 100644
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Binary files /dev/null and b/inst/peg3_lower_case.bam.bai differ
tests/testthat/test-plot_basic.R
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@@ -2,6 +2,15 @@ test_that("Plotting gene works", {
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     # setup
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     nmr <- load_example_nanomethresult()
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     mbr <- load_example_modbamresult()
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+
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+    mbr_lower <- load_example_modbamresult()
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+    methy(mbr_lower) <- ModBamFiles(
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+        paths = system.file(package = "NanoMethViz", "peg3_lower_case.bam"),
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+        samples = "sample1"
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+    )
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+
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+    data_list <- list(nmr, mbr, mbr_lower)
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+
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     params <- expand.grid(
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         heatmap = c(TRUE, FALSE),
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         spaghetti = c(TRUE, FALSE),
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@@ -9,7 +18,7 @@ test_that("Plotting gene works", {
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     )
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     # test plot_gene() ----
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-    for (x in list(nmr, mbr)) {
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+    for (x in data_list) {
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         expect_silent(p <- plot_gene(x, "Peg3"))
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         expect_s3_class(p, "ggplot")
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... ... 
@@ -44,7 +53,7 @@ test_that("Plotting gene works", {
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     }
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     # test plot_region() ----
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-    for (x in list(nmr, mbr)) {
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+    for (x in data_list) {
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         expect_silent(p <- plot_region(x, "chr7", 6703892, 6730431))
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         expect_s3_class(p, "ggplot")
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... ... 
@@ -75,7 +84,7 @@ test_that("Plotting gene works", {
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     # test plot_grange() ----
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     grange <- GenomicRanges::GRanges("chr7:6703892-6730431")
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-    for (x in list(nmr, mbr)) {
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+    for (x in data_list) {
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         for (i in 1:nrow(params)) {
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             expect_silent(
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                 p <- plot_grange(