platetools (version 0.1.7)

bhit_map: Platemap to identify 'hits' following a B-score normalisation

Description

Produces a platemap with colours indicating wells above or below selected threshold after normalising for systematic plate effects via B-score smooth. The threshold is definined calculated from a z-score, i.e plus or minus standard deviations from the plate mean.

Usage

bhit_map(
  data,
  well,
  plate = 96,
  threshold = 2,
  palette = "Spectral",
  eps = 0.01,
  maxiter = 10,
  trace.iter = FALSE,
  na.rm = TRUE,
  ...
)

Value

ggplot plot

Arguments

data

Vector of numerical values

well

Vector of well identifiers, e.g "A01"

plate

Number of wells in whole plate (96, 384 or 1536)

threshold

Standard deviations from the plate average to indicate a hit. default is set to +/- 2 SD.

palette

RColorBrewer palette

eps

real number greater than 0. A tolerance for divergence

maxiter

int, the maximum number of iterations

trace.iter

Boolean, should progress in convergence be reported?

na.rm

Boolean, should missing values be removed?

...

additional parameters to plot wrappers

Examples

df <- data.frame(vals = rnorm(384),
   well = num_to_well(1:384, plate = 384))

bhit_map(data = df$vals,
   well = df$well,
   plate = 384,
   threshold = 3)