Plotting a PCR attribute in the PCR plate design

Plots an attribute of PCRs from a metabarlist object into the corresponding 96-well PCR plate design

ggpcrplate(
  metabarlist,
  legend_title = "well_values",
  FUN = function(metabarlist) {
     rowSums(metabarlist$reads)
 }
)

Arguments

metabarlist: a metabarlist object.
legend_title: the title of legend containing the plotted information.
FUN: a function which returns a vector containing the information to be plotted. The vector should be numeric and of equal length to the number of rows of the `reads` table.

Value

a ggplot

Details

Visualising PCR attributes in their plate design context, i.e. their location in one or a set of 96-well PCR plates. This can be useful for identifying potential problems (e.g. high amount of reads in one control due to cross contaminations with neighboring samples).

Author

Lucie Zinger, Clément Lionnet

Examples


data(soil_euk)

## Plot the number of reads per pcr
ggpcrplate(soil_euk)



## Plot the number of reads of the most abundant MOTU
ggpcrplate(soil_euk,
  legend_title = "#reads of most \nabundant MOTU",
  FUN = function(m) {
    m$reads[, which.max(colSums(m$reads))]
  }
)