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

Objective

Include design_draw_libsize_qq() to Hermes by updating and replacing the draw_qq() function from rnaseqTools to use ggplot2, use an HermesData object as input.

Idea

In order to plot the sample against theoretical queantiles of library size in a QQ plot, 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))

# Check the class
is_class(result, 'AnyHermesData')

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

#QQ Plot
ggplot(df, aes(sample=libsize)) +
  stat_qq() +
  stat_qq_line() +
  theme_classic() +
  ggtitle("QQ plot of Library Sizes") +
  xlab("Theoretical Quantiles") +
   ylab("Sample Quantiles") +
  theme(plot.title = element_text(hjust = 0.5, face = "bold")) 

# design_draw_libsize_qq Function 
design_draw_libsize_qq <- function(object, ...) {
  assert_that(
    is_class(object, "AnyHermesData")
  )
  df <- data.frame(libsize = colSums(counts(result)))

  ggplot(df, aes(sample=libsize)) +
  stat_qq() +
  stat_qq_line() +
  theme_classic() +
  ggtitle("QQ plot of Library Sizes") +
  xlab("Theoretical Quantiles") +
   ylab("Sample Quantiles") +
  theme(plot.title = element_text(hjust = 0.5, face = "bold")) 
}

insightsengineering/hermes documentation built on March 11, 2024, 11:04 p.m.