In insightsengineering/hermes: Preprocessing, analyzing, and reporting of RNA-seq data

Objective

Update and replace the draw_hist() function from rnaseqTools to use ggplot2 and use an HermesData object as input.

Idea

In order to plot the library depth, we need to access the counts data in the HermesData object.

#Creating the HermesData object from the example SummarizedExperiment object.
result <- hermes_data

#Accessing the counts data.
counts(result)

#Calculating the library depth per sample.
colSums(counts(result))

#Coercing the library depth into a data frame because ggplot requires a data frame object.
df <- as.data.frame(colSums(counts(result)))

#Putting the final function together.
draw_libsize_hist <- function(object, bins, ...){
  df <- as.data.frame(colSums(counts(object)))
  ggplot(df, aes(colSums(counts(result)))) +
    geom_histogram(color = "white", bins = bins) +
    stat_bin(bins = bins, geom = "text", aes(label = ifelse(..count.. > 0, ..count.., "")), vjust = -0.25) +
    ggtitle("Histogram of Library Sizes") +
    xlab("Library Depth") +
    ylab("Frequency")
}

#Running the function.
draw_libsize_hist(result, 30)

insightsengineering/hermes documentation built on Jan. 25, 2025, 6:21 a.m.