Change order of samples in metData object

[beantkapoor786]

Hello, thank you for building this useful R package. I have made various plots using alignment files and vcf metrics using the PHGmetrics constructor object metData. I was wondering if there is any way to change the order of the samples in this object and subsequently in the generated plots? Thank you.

[btmonier]

Sorry for the late reply. We currently do not have a simple parameter to pass to the base plot functions, but since these plot objects are modified ggplot objects, we can directly manipulate the data slots for each sub-plot. Here is a reprex for manipulating gVCF plots:

# Get test data and plot
metBase <- system.file(
    "extdata", "toy_gvcf_metrics.tsv", 
    package = "rPHG2"
) |>
    PHGMetrics()

pBase <- metBase |> plotGvcf()

# New sample order
newOrder <- c("Xb02", "Xb03", "Xb01") # old levels (Xb01, Xb02, Xb03)

# Make in-memory copy
pNewOrder <- pBase

# Re-order copy
for(i in seq_len(length(pNewOrder))) {
    pNewOrder[[i]]$data$taxa <- factor(
        pNewOrder[[i]]$data$taxa, 
        levels = newOrder
    )
}

# Inspect
pNewOrder