R/browser_default.R
In Miswi/RiboCrypt: Interactive visualization in genomics
Defines functions
multiOmicsPlot_animate
multiOmicsPlot_list
Documented in
multiOmicsPlot_animate
multiOmicsPlot_list
#' Multi-omics plot using list input
#'
#' Customizable html plots for visualizing genomic data.
#' @param display_range the whole region to visualize,
#' a \code{\link[GenomicRanges]{GRangesList}} or \code{\link[GenomicRanges]{GRanges}} object
#' @param annotation the whole annotation which your target region is a subset,
#' a \code{\link[GenomicRanges]{GRangesList}} or \code{\link[GenomicRanges]{GRanges}} object
#' @param reference_sequence the genome reference,
#' a \code{\link[Rsamtools]{FaFile}} or \code{\link[Rsamtools]{FaFile}} convertible object
#' @param reads the NGS libraries, as a list of \code{\link[GenomicRanges]{GRanges}} with or without score column for replicates.
#' @param viewMode character, default "tx" (transcript coordinates, first position is 1,
#' exons are merged into a single sequence)\cr
#' Alternative: "genomic" (genomic coordinates, first position is first position in
#' \code{display_range} argument. Introns are displayed).
#' @param custom_regions a GRangesList or NULL, default: NULL.
#' The alternative annotation, like self defined uORFs etc. The vertical annotation bars will have
#' a different color.
#' @param leader_extension integer, default 0. (How much to extend view upstream)
#' @param trailer_extension integer, default 0. (How much to extend view downstream)
#' @param withFrames a logical vector, default NULL. Alternative: a length 1 or same length as list length of "reads" argument.
#' @param frames_type character, default "lines". Alternative:\cr
#' - columns \cr
#' - stacks \cr
#' - area
#' @param colors character, default NULL (automatic colouring). If "withFrames" argument
#' is TRUE, colors are set to to c("red", "green", "blue") for the 3 frames.
#' Alternative: Character vector of length 1 or length of "reads" list argument.
#' @param kmers numeric (integer), bin positions into kmers.
#' @param kmers_type character, function used for kmers sliding window. default: "mean", alternative: "sum"
#' @param ylabels character, default NULL. Name of libraries in "reads" list arugment.
#' @param width numeric, default NULL. Width of plot.
#' @param height numeric, default NULL. Height of plot.
#' @param plot_name = character, default "default" (will create name from display_range name).
#' Alternative: custom name for region.
#' @param plot_title character, default NULL. A title for plot.
#' @param display_sequence character/logical, default \code{c("both","nt", "aa", "none")[1]}.
#' If TRUE or "both", display nucleotide and aa sequence in plot.
#' @param annotation_names character, default NULL. Alternative naming for annotation.
#' @param seq_render_dist integer, default 100. The sequences will appear after zooming below this threshold.
#' @param aa_letter_code character, when set to "three_letters", three letter amino acid code is used. One letter by default.
#' @param lib_to_annotation_proportions numeric vector of length 2. relative sizes of profiles and annotation.
#' @param lib_proportions numeric vector of length equal to displayed libs. Relative sizes of profiles displayed
#' @param summary_track_type character, default is same as 'frames_type'
#' argument
#' @param annotation_proportions numeric vector of length 3 (seq displayed), or 2 (seq not displayed). Relative sizes of annotation tracks.
#' @param summary_track logical, default FALSE. Display a top track, that is the sum
#' of all tracks.
#' @param AA_code Genetic code for amino acid display. Default is SGC0 (standard: Vertebrate).
#' See \code{Biostrings::GENETIC_CODE_TABLE} for options. To change to bacterial, do:
#' \code{Biostrings::getGeneticCode("11")}
#' @param log_scale logical, default FALSE. Log2 scale the count values, for easier visualization of shapes.
#' @param BPPARAM how many cores/threads to use? default: \code{BiocParallel::SerialParam()}.
#' To see number of threads used for multicores, do \code{BiocParallel::bpparam()$workers}.
#' You can also add a time remaining bar, for a more detailed pipeline.
#' @param export.format character, default: "svg". alternative: "png".
#' when you click the top right image button export, what should it export as?
#' @inheritParams createSeqPanelPattern
#' @return the plot object
#' @importFrom GenomicFeatures extractTranscriptSeqs
#' @importFrom BiocParallel bpparam bpmapply
#' @importFrom Biostrings GENETIC_CODE
#' @export
#' @examples
#' library(RiboCrypt)
#' df <- ORFik.template.experiment()[9:10,]
#' cds <- loadRegion(df, "cds")
#' mrna <- loadRegion(df, "mrna")
#' multiOmicsPlot_list(mrna[1], annotation = cds[1], reference_sequence = findFa(df),
#' frames_type = "columns", leader_extension = 30, trailer_extension = 30,
#' reads = outputLibs(df, type = "pshifted", output.mode = "envirlist",
#' naming = "full", BPPARAM = BiocParallel::SerialParam()))
multiOmicsPlot_list <- function(display_range, annotation = display_range, reference_sequence,
reads, viewMode = c("tx", "genomic")[1], custom_regions = NULL,
leader_extension = 0, trailer_extension = 0,
withFrames = NULL,
frames_type = "lines", colors = NULL,
kmers = NULL, kmers_type = c("mean", "sum")[1],
ylabels = NULL, lib_to_annotation_proportions = c(0.8,0.2),
lib_proportions = NULL, annotation_proportions = NULL,
width = NULL, height = NULL, plot_name = "default",
plot_title = NULL,
display_sequence = c("both","nt", "aa", "none")[1], seq_render_dist = 100,
aa_letter_code = c("one_letter", "three_letters")[1],
annotation_names = NULL,
start_codons = "ATG", stop_codons = c("TAA", "TAG", "TGA"),
custom_motif = NULL, AA_code = Biostrings::GENETIC_CODE,
log_scale = FALSE, BPPARAM = BiocParallel::SerialParam(), summary_track = FALSE,
summary_track_type = frames_type,
export.format = "svg") {
multiOmicsPlot_internal(display_range, df = NULL, annotation,reference_sequence,
reads,
viewMode,
custom_regions,
leader_extension, trailer_extension,
withFrames,
frames_type, colors, kmers, kmers_type,
ylabels, lib_to_annotation_proportions,lib_proportions,
annotation_proportions,width, height,
plot_name, plot_title,
display_sequence, seq_render_dist,
aa_letter_code,
annotation_names, start_codons, stop_codons,
custom_motif, log_scale, BPPARAM, "",
summary_track, summary_track_type, export.format)
}
#' Multi-omics animation using list input
#'
#' The animation will move with a play butten, there is
#' 1 transition per library given.
#' @inheritParams multiOmicsPlot_list
#' @return the plot object
#' @export
#' @examples
#' library(RiboCrypt)
#' df <- ORFik.template.experiment()[9:10,]
#' cds <- loadRegion(df, "cds")
#' mrna <- loadRegion(df, "mrna")
#' # multiOmicsPlot_animate(mrna[1], annotation = cds[1], reference_sequence = findFa(df),
#' # frames_type = "columns", leader_extension = 30, trailer_extension = 30,
#' # reads = outputLibs(df, type = "pshifted", output.mode = "envirlist",
#' # naming = "full", BPPARAM = BiocParallel::SerialParam()))
multiOmicsPlot_animate <- function(display_range, annotation = display_range, reference_sequence,
reads, viewMode = c("tx", "genomic")[1], custom_regions = NULL,
leader_extension = 0, trailer_extension = 0,
withFrames = NULL,
frames_type = "lines", colors = NULL,
kmers = NULL, kmers_type = c("mean", "sum")[1],
ylabels = NULL, lib_to_annotation_proportions = c(0.8,0.2),
lib_proportions = NULL, annotation_proportions = NULL,
width = NULL, height = NULL, plot_name = "default",
plot_title = NULL,
display_sequence = c("both","nt", "aa", "none")[1], seq_render_dist = 100,
aa_letter_code = c("one_letter", "three_letters")[1],
annotation_names = NULL,
start_codons = "ATG", stop_codons = c("TAA", "TAG", "TGA"),
custom_motif = NULL, log_scale = FALSE,
BPPARAM = BiocParallel::SerialParam()) {
multiOmicsController()
# Get sequence and create basic seq panel
target_seq <- extractTranscriptSeqs(reference_sequence, display_range)
read_names <- names(reads) # Names for frames for seq panels
seq_panel <- createSeqPanelPattern(
target_seq[[1]], start_codons = start_codons,
stop_codons = stop_codons, custom_motif = custom_motif,
frame = read_names)
# Get the panel for the annotation track
gene_model_panel <- createGeneModelPanel(display_range, annotation,
custom_regions = custom_regions,
viewMode = viewMode,
frame = read_names)
lines <- gene_model_panel[[2]]
gene_model_panel <- gene_model_panel[[1]]
# profiles <- mapply(function(x,y,z) getProfileAnimate(display_range, x, y, z, kmers_type),
# reads, withFrames, kmers, SIMPLIFY = FALSE)
profiles <- bpmapply(function(x,y,z) getProfileAnimate(display_range, x, y, z, kmers_type),
reads, withFrames, kmers, SIMPLIFY = FALSE, BPPARAM = BPPARAM)
profiles <- rbindlist(profiles, idcol = "file")
plot <- list(getPlotAnimate(profiles, withFrames = withFrames[1],
colors = colors[1], ylabels = ylabels[1], lines = lines))
if (display_sequence %in% c("none", FALSE)){
plots <- c(plot, list(automateTicksGMP(gene_model_panel), automateTicksX(seq_panel)))
multiomics_plot <- subplot(plots,
margin = 0,
nrows = 3,
heights = c(0.8, 0.05, 0.15),
shareX = TRUE,
titleY = TRUE, titleX = TRUE)
} else {
nplots <- length(plot)
nt_area <- ggplot() +
theme(axis.title = element_blank(),
axis.ticks = element_blank(),
axis.text = element_blank()) +
theme(plot.margin = unit(c(0,0,0,0), "pt"))+
scale_x_continuous(expand = c(0,0))
plots <- c(plot, list(automateTicks(nt_area), automateTicksGMP(gene_model_panel),
automateTicksX(seq_panel)))
multiomics_plot <- subplot(plots,
margin = 0,
nrows = 4,
heights = c(0.7, 0.05, 0.15, 0.1),
shareX = TRUE,
titleY = TRUE,
titleX = TRUE)
}
multiomics_plot <- lineDeSimplify(multiomics_plot)
multiomics_plot <- multiomics_plot %>% plotly::config(
toImageButtonOptions = list(
format = "svg",
filename = ifelse(plot_name == "default",names(display_range),plot_name),
width = width,
height = height))
if (!is.null(plot_title)) multiomics_plot <- multiomics_plot %>% plotly::layout(title = plot_title)
return(multiomics_plot)
}
Miswi/RiboCrypt documentation built on April 16, 2024, 10:47 a.m.
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Defines functions multiOmicsPlot_animate multiOmicsPlot_list
Documented in multiOmicsPlot_animate multiOmicsPlot_list
#' Multi-omics plot using list input
#'
#' Customizable html plots for visualizing genomic data.
#' @param display_range the whole region to visualize,
#' a \code{\link[GenomicRanges]{GRangesList}} or \code{\link[GenomicRanges]{GRanges}} object
#' @param annotation the whole annotation which your target region is a subset,
#' a \code{\link[GenomicRanges]{GRangesList}} or \code{\link[GenomicRanges]{GRanges}} object
#' @param reference_sequence the genome reference,
#' a \code{\link[Rsamtools]{FaFile}} or \code{\link[Rsamtools]{FaFile}} convertible object
#' @param reads the NGS libraries, as a list of \code{\link[GenomicRanges]{GRanges}} with or without score column for replicates.
#' @param viewMode character, default "tx" (transcript coordinates, first position is 1,
#' exons are merged into a single sequence)\cr
#' Alternative: "genomic" (genomic coordinates, first position is first position in
#' \code{display_range} argument. Introns are displayed).
#' @param custom_regions a GRangesList or NULL, default: NULL.
#' The alternative annotation, like self defined uORFs etc. The vertical annotation bars will have
#' a different color.
#' @param leader_extension integer, default 0. (How much to extend view upstream)
#' @param trailer_extension integer, default 0. (How much to extend view downstream)
#' @param withFrames a logical vector, default NULL. Alternative: a length 1 or same length as list length of "reads" argument.
#' @param frames_type character, default "lines". Alternative:\cr
#' - columns \cr
#' - stacks \cr
#' - area
#' @param colors character, default NULL (automatic colouring). If "withFrames" argument
#' is TRUE, colors are set to to c("red", "green", "blue") for the 3 frames.
#' Alternative: Character vector of length 1 or length of "reads" list argument.
#' @param kmers numeric (integer), bin positions into kmers.
#' @param kmers_type character, function used for kmers sliding window. default: "mean", alternative: "sum"
#' @param ylabels character, default NULL. Name of libraries in "reads" list arugment.
#' @param width numeric, default NULL. Width of plot.
#' @param height numeric, default NULL. Height of plot.
#' @param plot_name = character, default "default" (will create name from display_range name).
#' Alternative: custom name for region.
#' @param plot_title character, default NULL. A title for plot.
#' @param display_sequence character/logical, default \code{c("both","nt", "aa", "none")[1]}.
#' If TRUE or "both", display nucleotide and aa sequence in plot.
#' @param annotation_names character, default NULL. Alternative naming for annotation.
#' @param seq_render_dist integer, default 100. The sequences will appear after zooming below this threshold.
#' @param aa_letter_code character, when set to "three_letters", three letter amino acid code is used. One letter by default.
#' @param lib_to_annotation_proportions numeric vector of length 2. relative sizes of profiles and annotation.
#' @param lib_proportions numeric vector of length equal to displayed libs. Relative sizes of profiles displayed
#' @param summary_track_type character, default is same as 'frames_type'
#' argument
#' @param annotation_proportions numeric vector of length 3 (seq displayed), or 2 (seq not displayed). Relative sizes of annotation tracks.
#' @param summary_track logical, default FALSE. Display a top track, that is the sum
#' of all tracks.
#' @param AA_code Genetic code for amino acid display. Default is SGC0 (standard: Vertebrate).
#' See \code{Biostrings::GENETIC_CODE_TABLE} for options. To change to bacterial, do:
#' \code{Biostrings::getGeneticCode("11")}
#' @param log_scale logical, default FALSE. Log2 scale the count values, for easier visualization of shapes.
#' @param BPPARAM how many cores/threads to use? default: \code{BiocParallel::SerialParam()}.
#' To see number of threads used for multicores, do \code{BiocParallel::bpparam()$workers}.
#' You can also add a time remaining bar, for a more detailed pipeline.
#' @param export.format character, default: "svg". alternative: "png".
#' when you click the top right image button export, what should it export as?
#' @inheritParams createSeqPanelPattern
#' @return the plot object
#' @importFrom GenomicFeatures extractTranscriptSeqs
#' @importFrom BiocParallel bpparam bpmapply
#' @importFrom Biostrings GENETIC_CODE
#' @export
#' @examples
#' library(RiboCrypt)
#' df <- ORFik.template.experiment()[9:10,]
#' cds <- loadRegion(df, "cds")
#' mrna <- loadRegion(df, "mrna")
#' multiOmicsPlot_list(mrna[1], annotation = cds[1], reference_sequence = findFa(df),
#' frames_type = "columns", leader_extension = 30, trailer_extension = 30,
#' reads = outputLibs(df, type = "pshifted", output.mode = "envirlist",
#' naming = "full", BPPARAM = BiocParallel::SerialParam()))
multiOmicsPlot_list <- function(display_range, annotation = display_range, reference_sequence,
reads, viewMode = c("tx", "genomic")[1], custom_regions = NULL,
leader_extension = 0, trailer_extension = 0,
withFrames = NULL,
frames_type = "lines", colors = NULL,
kmers = NULL, kmers_type = c("mean", "sum")[1],
ylabels = NULL, lib_to_annotation_proportions = c(0.8,0.2),
lib_proportions = NULL, annotation_proportions = NULL,
width = NULL, height = NULL, plot_name = "default",
plot_title = NULL,
display_sequence = c("both","nt", "aa", "none")[1], seq_render_dist = 100,
aa_letter_code = c("one_letter", "three_letters")[1],
annotation_names = NULL,
start_codons = "ATG", stop_codons = c("TAA", "TAG", "TGA"),
custom_motif = NULL, AA_code = Biostrings::GENETIC_CODE,
log_scale = FALSE, BPPARAM = BiocParallel::SerialParam(), summary_track = FALSE,
summary_track_type = frames_type,
export.format = "svg") {
multiOmicsPlot_internal(display_range, df = NULL, annotation,reference_sequence,
reads,
viewMode,
custom_regions,
leader_extension, trailer_extension,
withFrames,
frames_type, colors, kmers, kmers_type,
ylabels, lib_to_annotation_proportions,lib_proportions,
annotation_proportions,width, height,
plot_name, plot_title,
display_sequence, seq_render_dist,
aa_letter_code,
annotation_names, start_codons, stop_codons,
custom_motif, log_scale, BPPARAM, "",
summary_track, summary_track_type, export.format)
}
#' Multi-omics animation using list input
#'
#' The animation will move with a play butten, there is
#' 1 transition per library given.
#' @inheritParams multiOmicsPlot_list
#' @return the plot object
#' @export
#' @examples
#' library(RiboCrypt)
#' df <- ORFik.template.experiment()[9:10,]
#' cds <- loadRegion(df, "cds")
#' mrna <- loadRegion(df, "mrna")
#' # multiOmicsPlot_animate(mrna[1], annotation = cds[1], reference_sequence = findFa(df),
#' # frames_type = "columns", leader_extension = 30, trailer_extension = 30,
#' # reads = outputLibs(df, type = "pshifted", output.mode = "envirlist",
#' # naming = "full", BPPARAM = BiocParallel::SerialParam()))
multiOmicsPlot_animate <- function(display_range, annotation = display_range, reference_sequence,
reads, viewMode = c("tx", "genomic")[1], custom_regions = NULL,
leader_extension = 0, trailer_extension = 0,
withFrames = NULL,
frames_type = "lines", colors = NULL,
kmers = NULL, kmers_type = c("mean", "sum")[1],
ylabels = NULL, lib_to_annotation_proportions = c(0.8,0.2),
lib_proportions = NULL, annotation_proportions = NULL,
width = NULL, height = NULL, plot_name = "default",
plot_title = NULL,
display_sequence = c("both","nt", "aa", "none")[1], seq_render_dist = 100,
aa_letter_code = c("one_letter", "three_letters")[1],
annotation_names = NULL,
start_codons = "ATG", stop_codons = c("TAA", "TAG", "TGA"),
custom_motif = NULL, log_scale = FALSE,
BPPARAM = BiocParallel::SerialParam()) {
multiOmicsController()
# Get sequence and create basic seq panel
target_seq <- extractTranscriptSeqs(reference_sequence, display_range)
read_names <- names(reads) # Names for frames for seq panels
seq_panel <- createSeqPanelPattern(
target_seq[[1]], start_codons = start_codons,
stop_codons = stop_codons, custom_motif = custom_motif,
frame = read_names)
# Get the panel for the annotation track
gene_model_panel <- createGeneModelPanel(display_range, annotation,
custom_regions = custom_regions,
viewMode = viewMode,
frame = read_names)
lines <- gene_model_panel[[2]]
gene_model_panel <- gene_model_panel[[1]]
# profiles <- mapply(function(x,y,z) getProfileAnimate(display_range, x, y, z, kmers_type),
# reads, withFrames, kmers, SIMPLIFY = FALSE)
profiles <- bpmapply(function(x,y,z) getProfileAnimate(display_range, x, y, z, kmers_type),
reads, withFrames, kmers, SIMPLIFY = FALSE, BPPARAM = BPPARAM)
profiles <- rbindlist(profiles, idcol = "file")
plot <- list(getPlotAnimate(profiles, withFrames = withFrames[1],
colors = colors[1], ylabels = ylabels[1], lines = lines))
if (display_sequence %in% c("none", FALSE)){
plots <- c(plot, list(automateTicksGMP(gene_model_panel), automateTicksX(seq_panel)))
multiomics_plot <- subplot(plots,
margin = 0,
nrows = 3,
heights = c(0.8, 0.05, 0.15),
shareX = TRUE,
titleY = TRUE, titleX = TRUE)
} else {
nplots <- length(plot)
nt_area <- ggplot() +
theme(axis.title = element_blank(),
axis.ticks = element_blank(),
axis.text = element_blank()) +
theme(plot.margin = unit(c(0,0,0,0), "pt"))+
scale_x_continuous(expand = c(0,0))
plots <- c(plot, list(automateTicks(nt_area), automateTicksGMP(gene_model_panel),
automateTicksX(seq_panel)))
multiomics_plot <- subplot(plots,
margin = 0,
nrows = 4,
heights = c(0.7, 0.05, 0.15, 0.1),
shareX = TRUE,
titleY = TRUE,
titleX = TRUE)
}
multiomics_plot <- lineDeSimplify(multiomics_plot)
multiomics_plot <- multiomics_plot %>% plotly::config(
toImageButtonOptions = list(
format = "svg",
filename = ifelse(plot_name == "default",names(display_range),plot_name),
width = width,
height = height))
if (!is.null(plot_title)) multiomics_plot <- multiomics_plot %>% plotly::layout(title = plot_title)
return(multiomics_plot)
}
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