Overlay a peak list to a plot

Overlay a peak list to a plot

overlay_peaklist(
  peaklist = NULL,
  ...,
  dt_range = NULL,
  rt_range = NULL,
  pdata = NULL,
  color_by = NULL,
  mapping_roi = c(dt_min_ms = "dt_min_ms", dt_max_ms = "dt_max_ms", rt_min_s =
    "rt_min_s", rt_max_s = "rt_max_s"),
  palette = P40
)

Arguments

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)

...

Ignored.

dt_range

The minimum and maximum drift times to extract (length 2 vector)

rt_range

The minimum and maximum retention times to extract (length 2 vector)

pdata

A phenotype data data frame, with a SampleID column. This column will be used to merge pdata with peaklist, so color_by can specify a phenotype.

color_by

A character with a column name of peaklist or pdata. Used to color the border of the added rectangles and apices. A string with a color name is also acceptable.

mapping_roi

A 4-elements named character vector with the names of the columns from peaklist that will be used as the rectangle coordinates.

palette

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

Value

A list with the ggplot layers to overlay, including geom_rect and possibly geom_point and scale_fill_manual.

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
)

plt + overlay_peaklist(
  peaklist = rect
)