Helper values and functions

Let us first define some values useful to design colour scales:

range.exprs <- range(assay(sce.endo, "logcounts"))
col.treatment <- RColorBrewer::brewer.pal(9, "Paired")[c(9,3,4,1,2)]
names(col.treatment) <- gsub("_","\n",levels(sce.endo$TreatmentLabel))

Let us then define a few convenience functions:

• to fetch the gene ID associated with a gene name

geneNameToID <- function(x){
  geneId <- subset(rowData(sce.endo), gene_name == x, "gene_id", drop = TRUE)
  if (length(geneId) > 1){
    warning("Multiple IDs found. Use ID instead")
    return(data.frame(
      gene_name = x,
      gene_id = geneId
    ))
  } else if (length(geneId) == 0){
    stop("gene_name not found")
  }
  return(geneId)
}

• to fetch the necessary expression and phenotype data

geneDataByName <- function(x){
  geneId <- geneNameToID(x)
  ggData <- data.frame(
    gene = assay(sce.endo, "logcounts")[geneId,],
    colData(sce.endo)[,c("Time","Infection","Status","TreatmentLabel")]
  )
  return(ggData)
}

• to draw the figure, faceted by time

plotByNameFacetTime <- function(x){
  geneId <- geneNameToID(x)
  ggData <- geneDataByName(x)
  # return(ggData)
  ggplot(ggData, aes(TreatmentLabel, gene)) +
    facet_grid(Time~.) +
    geom_violin(
      aes(colour = TreatmentLabel, fill = TreatmentLabel),
      alpha = 0.2) +
    geom_jitter(
      aes(colour = TreatmentLabel), height = 0, width = 0.2,
      alpha = 0.5, size = 0.4) +
    scale_color_manual(values = col.treatment) +
    scale_fill_manual(values = col.treatment) +
    labs(
      title = sprintf("%s", x),
      subtitle = sprintf("%s", geneId),
      x = "Treatment",
      y = "log-counts",
      colour = "Treatment",
      fill = "Treatment") +
    scale_y_continuous(limits = range.exprs) +
    theme_bw() +
    theme(
      legend.key.height = unit(1.75, "lines")
    )
}

• to draw the figure, for a single time point

plotByNameSubset <- function(
  x,
  time = c("2h","4h","6h"),
  infection = c("Mock","STM-LT2","STM-D23580"),
  status = c("Uninfected","Exposed","Infected")
  ){
  geneId <- geneNameToID(x)
  ggData <- geneDataByName(x)
  ggData <- subset(
    ggData,
    Time %in% time & Infection %in% infection & Status %in% status)
  # return(ggData)
  ggplot(ggData, aes(TreatmentLabel, gene)) +
    geom_violin(
      aes(colour = TreatmentLabel, fill = TreatmentLabel), scale = "width",
      alpha = 0.4) +
    geom_jitter(
      aes(colour = TreatmentLabel), height = 0, width = 0.2,
      alpha = 0.5, size = 0.4) +
    scale_color_manual(values = col.treatment) +
    scale_fill_manual(values = col.treatment) +
    labs(
      title = sprintf("%s (%s)", x, time),
      subtitle = sprintf("%s", geneId),
      x = "Treatment",
      y = "log-counts",
      colour = "Treatment",
      fill = "Treatment") +
    scale_y_continuous(limits = range.exprs) +
    theme_bw() +
    theme(
      legend.key.height = unit(1.75, "lines"),
      axis.text.y = element_text(size = rel(1.5)),
      panel.grid.minor = element_blank()
    )
}