Add peak list rectangles to a raw plot

Add peak list rectangles to a raw plot

add_peaklist_rect(
  plt,
  peaklist,
  color_by = NULL,
  col_prefix = "",
  pdata = NULL,
  palette = P40
)

Arguments

plt

The output of plot() when applied to a GCIMSSample

peaklist

A data frame with at least the columns: dt_min_ms, dt_max_ms, rt_min_s, rt_max_s and optionally additional columns (e.g. the column given to color_by)

color_by

A character with a column name of peaklist. Used to color the border of the added rectangles

col_prefix

After clustering, besides dt_min_ms, we also have

pdata

A phenotype data data frame, with a SampleID column to be merged into peaklist so color_by can specify a phenotype freesize_dt_min_ms. Use col_prefix = "freesize_" to plot the freesize version

palette

A character vector with color names to use drawing the rectangles. Use NULL to let ggplot2 set the defaults.

Value

The given plt with rectangles showing the ROIs and crosses showing the apexes

Details

If peaklist includes dt_apex_ms and rt_apex_s a cross will be plotted on the peak apex.

Examples

dt <- 1:10
rt <- 1:10
int <- matrix(0.0, nrow = length(dt), ncol = length(rt))

int[2, 4:8] <- c(.5, .5, 1, .5, 0.5)
int[3, 4:8] <- c(0.5, 2, 2, 2, 0.5)
int[4, 4:8] <- c(1, 2, 5, 2, 1)
int[5, 4:8] <- c(0.5, 2, 2, 2, 0.5)
int[6, 4:8] <- c(.5, .5, 1, .5, 0.5)

dummy_obj <-GCIMSSample(
  drift_time = dt,
  retention_time = rt,
  data = int
)
plt <- plot(dummy_obj)

# Add a rectangle on top of the plot
rect <- data.frame(
  dt_min_ms = 2.75,
  dt_max_ms = 5.6,
  rt_min_s = 4.6,
  rt_max_s = 7.4
)

add_peaklist_rect(
  plt = plt,
  peaklist = rect
)
#> Warning: `add_peaklist_rect` is deprecated
#> ℹ Replace `add_peaklist_rect(plt, peaklist)` with `plt +
#>   overlay_peaklist(peaklist)` instead