plotting modules from multiple samples

NAMESPACE

@@ -4,10 +4,10 @@ S3method(print,qctable)
 S3method(summary,qc_aggregate)
 export(fastqc)
 export(fastqc_install)
-export(plot_gc_content_collection)
 export(qc_aggregate)
 export(qc_fails)
 export(qc_plot)
+export(qc_plot_collection)
 export(qc_problems)
 export(qc_read)
 export(qc_read_collection)
@@ -21,6 +21,7 @@ importFrom(ggplot2,aes_string)
 importFrom(ggplot2,coord_cartesian)
 importFrom(ggplot2,element_text)
 importFrom(ggplot2,expand_limits)
+importFrom(ggplot2,facet_wrap)
 importFrom(ggplot2,geom_line)
 importFrom(ggplot2,geom_rect)
 importFrom(ggplot2,ggplot)

R/qc_plot_collection.R

@@ -1,28 +1,99 @@
-#' Plot GC content of a collection of samples
+#' @include utilities.R
+#' @importFrom ggplot2 ggplot
+#' @importFrom ggplot2 aes
+#' @importFrom ggplot2 aes_string
+#' @importFrom ggplot2 geom_line
+#' @importFrom ggplot2 theme_minimal
+#' @importFrom ggplot2 coord_cartesian
+#' @importFrom ggplot2 labs
+#' @importFrom ggplot2 theme
+#' @importFrom ggplot2 expand_limits
+#' @importFrom ggplot2 geom_rect
+#' @importFrom ggplot2 scale_x_discrete
+#' @importFrom ggplot2 coord_cartesian
+#' @importFrom ggplot2 element_text
+#' @importFrom ggplot2 facet_wrap
+NULL
+
+#' Plot FastQC Results of multiple samples
 #' 
-#' A working example of a function to plot the GC content of multiple samples as multiple lines.
+#' @description Plot FastQC data of multiple samples 
 #' 
-#' @param qc An object of class qc_read_collection
-#' @param ggtheme A plotting themem
-#' @param ... Other
-#'
-#' @author Mahmoud Shaaban, \email{mahmoud.s.fahmy@@students.kasralainy.edu.eg}
-#'
-#' @return A graph of mulitple lines each corresponds to the GC content from one sample.
+#' @param qc An object of class qc_read_collection or a path to the sample zipped fastqc result files.
+#' @inheritParams qc_plot
 #' 
-#' @examples 
-#' # extract paths to the demo files
+#' @author Mahmoud Ahmed, \email{[email protected]}
+#'
+#' @return Returns a list of ggplots containing the plot for specified modules..
+#' @examples
+# extract paths to the demo files
 #' qc.dir <- system.file("fastqc_results", package = "fastqcr")
 #' qc.files <- list.files(qc.dir, full.names = TRUE)
 #' 
 #' # read all modules in all files
 #' qc <- qc_read_collection(qc.files, sample_names = paste('S', 1:5, sep = ''))
-#' 
-#' # plot GC content in all samples
-#' plot_gc_content_collection(qc)
-#' 
+#'
+#' # Plot per sequence GC content
+#' qc_plot_collection(qc, "Per sequence GC content")
+#'
+#' # Per base sequence quality
+#' qc_plot_collection(qc, "Per base sequence quality")
+#'
+#' # Per sequence quality scores
+#' qc_plot_collection(qc, "Per sequence quality scores")
+#'
+#' # Per base sequence content
+#' qc_plot_collection(qc, "Per base sequence content")
+#'
+#' # Sequence duplication levels
+#' qc_plot_collection(qc, "Sequence duplication levels")
+#'
 #' @export
-plot_gc_content_collection <- function(qc, ggtheme = theme_minimal(), ...){
+qc_plot_collection <- function(qc, modules = "all"){
+
+  if(inherits(qc, "character"))
+    qc <- qc_read(qc)
+  if(!inherits(qc, "qc_read_collection"))
+    stop("data should be an object of class qc_read_collection")
+
+  . <- NULL
+  modules <- .valid_fastqc_modules(modules) %>%
+    tolower() %>%
+    gsub(" ", "_", .)
+
+  res <- lapply(modules,
+                function(module, qc){
+                  plot.func.collection <- .plot_funct_collection(module)
+                  plot.func.collection(qc)
+                },
+                qc
+  )
+
+  names(res) <- modules
+  if(length(res) == 1) res[[1]]
+  else res
+}
+
+# Extrcat the plotting function according to the module
+.plot_funct_collection <- function(module){
+
+  switch(module,
+         per_sequence_gc_content = .plot_gc_content_collection,
+         per_base_sequence_quality = .plot_base_quality_collection,
+         per_sequence_quality_scores = .plot_sequence_quality_collection,
+         per_base_sequence_content = .plot_sequence_content_collection,
+         sequence_duplication_levels = .plot_duplication_levels_collection,
+         basic_statistics = .plot_basic_stat,
+         sequence_length_distribution = .plot_seq_length_distribution_collection,
+         summary = .plot_summary,
+         per_base_n_content = .plot_N_content_collection,
+         adapter_content = .plot_adapter_content_collection,
+         function(x){NULL}
+  )
+}
+
+# Per sequence GC content
+.plot_gc_content_collection <- function(qc, ggtheme = theme_minimal(), ...){
   .names <- names(qc)
   if(!("per_sequence_gc_content" %in% .names))
     return(NULL)
@@ -34,4 +105,223 @@ plot_gc_content_collection <- function(qc, ggtheme = theme_minimal(), ...){
     geom_line() +
     labs(title = "Per sequence GC content", x = "Mean GC Content (%)")+
     theme_minimal()
+}
+
+
+# Per base N content
+.plot_N_content_collection <- function(qc, ggtheme = theme_minimal(), ...){
+  if(!("per_base_n_content" %in% names(qc)))
+    return(NULL)
+
+  . <- NULL
+
+  d <- qc$per_base_n_content
+  if(nrow(d) == 0) return(NULL)
+  colnames(d) <- make.names(colnames(d))
+  d$Base <- factor(d$Base, levels = unique(d$Base))
+
+  # Select some breaks
+  nlev <- nlevels(d$Base)
+  breaks <- scales::extended_breaks()(1:nlev)[-1] %>% # index
+    c(1, ., nlev) %>% # Add the minimum & the max
+    d$Base[.] %>% # Values
+    as.vector()
+
+
+  ggplot(d, aes_string(x = "Base", y = "N.Count", color = 'sample', group = 'sample')) +
+    geom_line() +
+    scale_x_discrete(breaks = breaks)+
+    coord_cartesian(ylim = c(0, 100))+
+    labs(title = "Per base N content", x = "Position in read (bp)",
+         y = "Frequency (%)",
+         subtitle = "N content across all bases")+
+    theme_minimal()
+}
+
+
+# Sequence Length Distribution
+.plot_seq_length_distribution_collection <- function(qc, ggtheme = theme_minimal(), ...){
+  if(!("sequence_length_distribution" %in% names(qc)))
+    return(NULL)
+
+  d <- qc$sequence_length_distribution
+  if(nrow(d) == 0) return(NULL)
+
+  ggplot(d, aes_string(x = "Length", y = "Count", color = 'sample'))+
+    geom_line() +
+    labs(title = "Sequence length distribution", x = "Sequence Length (pb)",
+         y = "Count",
+         subtitle = "Distribution of sequence lengths over all sequences")+
+    theme_minimal()
   }
+
+# Per base sequence quality
+.plot_base_quality_collection <- function(qc, ggtheme = theme_minimal(), ...){
+
+  .names <- names(qc)
+  if(!("per_base_sequence_quality" %in% .names))
+    return(NULL)
+  . <- NULL
+
+  d <- qc$per_base_sequence_quality
+  if(nrow(d) == 0) return(NULL)
+
+  colnames(d) <- make.names(colnames(d))
+  d$Base <- factor(d$Base, levels = unique(d$Base))
+  # Select some breaks
+  nlev <- nlevels(d$Base)
+  breaks <- scales::extended_breaks()(1:nlev)[-1] %>% # index
+    c(1, ., nlev) %>% # Add the minimum & the max
+    d$Base[.] %>% # Values
+    as.vector()
+
+
+  ggplot()+
+    geom_line(data = d, aes_string(x = "Base", y = "Median", group = 'sample', color = 'sample')) +
+    expand_limits(x = 0, y = 0)+
+    geom_rect(aes(xmin = 0, ymin = 0, ymax = 20, xmax = Inf),
+              fill = "red", alpha = 0.2)+
+    geom_rect(aes(xmin = 0, ymin = 20, ymax = 28, xmax = Inf),
+              fill = "yellow", alpha = 0.2)+
+    geom_rect(aes(xmin = 0, ymin = 28, ymax = Inf, xmax = Inf),
+              fill = "#00AFBB", alpha = 0.2)+
+    scale_x_discrete(breaks = breaks)+
+    labs(title = "Per base sequence quality", x = "Position in read (pb)",
+         y = "Median quality scores",
+         subtitle = "Red: low quality zone")+
+    theme_minimal()
+}
+
+# Per sequence quality scores
+.plot_sequence_quality_collection <- function(qc, ggtheme = theme_minimal(), status = NULL, ...){
+  .names <- names(qc)
+  if(!("per_sequence_quality_scores" %in% .names))
+    return(NULL)
+
+  d <- qc$per_sequence_quality_scores
+  if(nrow(d) == 0) return(NULL)
+
+  ggplot(d, aes_string(x = "Quality", y = "Count", color = 'sample'))+
+    geom_line() +
+    labs(title = "Per sequence quality scores",
+         subtitle = "Quality score distribution over all sequences",
+         x = "Mean Sequence Quality (Phred Score)")+
+    theme_minimal()
+}
+
+# Per base sequence content
+.plot_sequence_content_collection <- function(qc, ggtheme = theme_minimal(), ...){
+  .names <- names(qc)
+  if(!("per_base_sequence_content" %in% .names))
+    return(NULL)
+
+  . <- NULL
+
+  Base <- NULL
+  d <- qc$per_base_sequence_content
+  if(nrow(d) == 0) return(NULL)
+
+  d$Base <- factor(d$Base, levels = unique(d$Base))
+  d <- d %>%
+    tidyr::gather(key = "base_name", value = "Count", -Base, -sample)
+
+
+  # Select some breaks
+  nlev <- nlevels(d$Base)
+  breaks <- scales::extended_breaks()(1:nlev)[-1] %>% # index
+    c(1, ., nlev) %>% # Add the minimum & the max
+    d$Base[.] %>% # Values
+    as.vector()
+
+
+  ggplot(d, aes_string(x = "Base", y = "Count", group = "base_name", color = "base_name"))+
+    geom_line() +
+    scale_x_discrete(breaks = breaks)+
+    labs(title = "Per base sequence content",
+         subtitle = "Sequence content across all bases",
+         x = "Position in read (pb)", y = "Nucleotide frequency (%)",
+         color = "Nucleotide")+
+    coord_cartesian(ylim = c(0, 100))+
+    facet_wrap(~sample, ncol = 1, strip.position = 'right') +
+    theme_minimal() +
+    theme(legend.position = 'top', legend.direction = "horizontal")
+}
+
+
+# Sequence Duplication Levels
+.plot_duplication_levels_collection <- function(qc, ggtheme = theme_minimal(), ...){
+  .names <- names(qc)
+  if(!("per_base_sequence_content" %in% .names))
+    return(NULL)
+
+  . <- NULL
+  Duplication.Level <- NULL
+  d <- qc$sequence_duplication_levels
+  if(nrow(d) == 0) return(NULL)
+  colnames(d) <- make.names(colnames(d))
+  d$Duplication.Level <- factor(d$Duplication.Level, levels = unique(d$Duplication.Level))
+  d <- d %>%
+    tidyr::gather(key = "Dup", value = "pct", -Duplication.Level, -sample)
+
+  # Select some breaks
+  nlev <- nlevels(d$Duplication.Level)
+  breaks <- scales::extended_breaks()(1:nlev)[-1] %>% # index
+    c(1, ., nlev) %>% # Add the minimum & the max
+    d$Duplication.Level[.] %>% # Values
+    as.vector()
+
+
+  ggplot(d, aes_string(x = "Duplication.Level", y = "pct", group = "Dup", color = "Dup"))+
+    geom_line() +
+    # scale_x_discrete(breaks = breaks)+
+    labs(title = "Sequence Duplication Levels",
+         x = "Sequence Duplication Level", y = "Percentage",
+         color = "")+
+    facet_wrap(~sample, ncol = 1, strip.position = 'right') +
+    theme_minimal() +
+    theme(legend.position = 'top')
+}
+
+
+# Adapter Content
+.plot_adapter_content_collection <- function(qc, ggtheme = theme_minimal(), ...){
+  if(!("adapter_content" %in% names(qc)))
+    return(NULL)
+
+  Position <- NULL
+
+  d <-  qc$adapter_content
+  colnames(d) <- make.names(colnames(d))
+  d <- d %>%
+    tidyr::gather(key = "adapter", value = "value", -Position, -sample)
+  ggplot(d, aes_string(x = "Position", y = "value", group = "adapter", color = "adapter"))+
+    geom_line() +
+    labs(title = "Adapter content",
+         x = "Position in read (pb)", y = "% Adapter",
+         color = "")+
+    coord_cartesian(ylim = c(0, 100))+
+    facet_wrap(~sample, ncol = 1, strip.position = 'right') +
+    theme_minimal() +
+    theme(legend.position = 'top')
+}
+
+# Per tile sequence quality
+.plot_tile_seq_quality_collection <- function(qc, ...){
+  if(!("per_tile_sequence_quality" %in% names(qc)))
+    return(NULL)
+
+  d <-  qc$per_tile_sequence_quality
+  if(nrow(d) == 0) return(NULL)
+
+  d$Tile <- as.character(d$Tile)
+  d$Base <- factor(d$Base, levels = unique(d$Base))
+
+  ggplot(d, aes_string(x = "Base", y = "Tile", fill = "Mean"))+
+    ggplot2::geom_tile() +
+    labs(title = "Per tile sequence quality",
+         subtitle = "Quality per tile",
+         x = "Position in read (pb)") +
+    theme_minimal() +
+    theme(legend.position = 'top', legend.direction = 'horizontal') +
+    facet_wrap(~sample, ncol = 1, strip.position = 'right')
+}

R/qc_read_collection.R

@@ -6,7 +6,7 @@
 #' @param sample_names A \code{character} vector of length equals that of the first argument \code{files}
 #' @inheritParams qc_read
 #'
-#' @author Mahmoud Shaaban, \email{mahmoud.s.fahmy@@students.kasralainy.edu.eg}
+#' @author Mahmoud Ahmed, \email{[email protected]}
 #'
 #' @return A \code{list} of \code{tibbles} containing the data of specified modules form each file.
 #'