Visualize longitudinal data

Usage

gglongi(
  data,
  x_val,
  y_val,
  col_val,
  col_legend = TRUE,
  mean_line = TRUE,
  x_title = x_val,
  y_title = y_val,
  treatments = NA,
  scans = NA,
  events = NA,
  treatment_start,
  treatment_end,
  treatment_drug,
  scan_date,
  event_date
)

Arguments

data

The data.frame containing the data to be used for the visualization

x_val

A string referring to the name of the column to be visualized on the X axis.

y_val

A string referring to the name of the column to be visualized on the Y axis.

col_val

A string referring to the name of the column to be used to color the points on the plot.

col_legend

A boolean value. If TRUE, the color legend will be displayed.

mean_line

A boolean value. If TRUE, the mean values per time point will be calculated and added as a continuous line.

x_title

A string to be used as label for the X axis.

y_title

A string to be used as label for the X axis.

treatments

A data.frame containing treatment information. It should have 3 columns:

a column containing the name of the drug
a column containing the time information for the start of treatment
a column containing the time information for the end of treatment

scans

A data.frame containing information about scan dates. It should contain a column denoting the time for each scan.

events

A data.frame containing information on clinical events. It should contain the type of event and the associated timing for the event.

treatment_start

A string referring to the name of the column containing the treatment start data.

treatment_end

A string referring to the name of the column containing the treatment end data.

treatment_drug

A string referring to the name of the column containing the treatment drug.

scan_date

A string referring to the name of the column containing the scan date in the scans data frame.

event_date

A string referring to the name of the column containing the event date in the events data frame.

Value

A ggplot object.

Examples

mafs <- data.frame(time_from_baseline = c(0, 0, 0, 27, 27),
                   MAF = c(0, 0.009, 0.007, 0.012, 0.032),
                   Gene = c('BRAF', 'BRAF', 'BRAF', 'TP53', 'TP53'))

treatment = data.frame(Treatment_drug = c('Drug 1', 'Drug 2'),
                       start_from_baseline = c(0, 307),
                       stop_from_baseline = c(224, 538))

scans = data.frame(Scan_num = c(1, 2, 3),
                   Days_from_baseline = c(12, 247, 499))

clinical_events = data.frame(Event = c('Progression', 'Death'),
                             Days_from_baseline = c(273, 620))

gglongi(mafs, x_val = "time_from_baseline", y_val = "MAF", col_val = "Gene",
        col_legend = TRUE, mean_line = TRUE, x_title = "Days from baseline sample",
        y_title = "Mutant allele frequency", treatments = treatment, scans = scans,
        events = clinical_events, treatment_start = "start_from_baseline",
        treatment_end = "stop_from_baseline", treatment_drug = "Treatment_drug",
        scan_date = "Days_from_baseline", event_date = "Days_from_baseline")