Swimlane Plot — g_swimlane • osprey

Swimlane plot is often used in Early Development (ED) and displays individual patient bar plot with markers of events and patient level annotation

Usage

g_swimlane(
  bar_id,
  bar_length,
  sort_by = NULL,
  col_by = NULL,
  marker_id = NULL,
  marker_pos = NULL,
  marker_shape = NULL,
  marker_shape_opt = NULL,
  marker_color = NULL,
  marker_color_opt = NULL,
  anno_txt = NULL,
  xref_line = NULL,
  xtick_at = waiver(),
  xlab,
  title
)

Arguments

bar_id: vector of IDs to identify each bar
bar_length: numeric vector to be plotted as length for each bar
sort_by: vector to sort bars
col_by: vector to color bars
marker_id: vector of IDs to identify markers within each bar. Default is the same as bar_id.
marker_pos: numeric vector to specify position for each marker point
marker_shape: vector to specify shape for markers
marker_shape_opt: aesthetic values to map shape values (named vector to map shape values to each name)
marker_color: vector to specify color for markers
marker_color_opt: aesthetic values to map shape values (named vector to map shape values to each name)
anno_txt: dataframe of subject-level variables to be displayed as annotation on the left
xref_line: numeric vector to plot reference lines
xtick_at: optional break interval of bar length axis
xlab: label for bar length
title: string to be displayed as plot title

Value

plot object

Author

Ting Qi (qit3) qit3@gene.com

Examples

# Example 1
library(dplyr)
library(nestcolor)

ADSL <- osprey::rADSL[1:20, ]
ADRS <- filter(rADRS, PARAMCD == "OVRINV")
ANL <- left_join(ADSL, ADRS, by = c("STUDYID", "USUBJID"), multiple = "all")
anno_txt <- ADSL[, c("ARMCD", "SEX")]

g_swimlane(
  bar_id = ADSL$USUBJID,
  bar_length = as.integer(ADSL$TRTEDTM - ADSL$TRTSDTM),
  sort_by = ADSL$ARM,
  col_by = ADSL$ARM,
  marker_id = ANL$USUBJID,
  marker_pos = ANL$ADY,
  marker_shape = ANL$AVALC,
  marker_shape_opt = c("CR" = 16, "PR" = 17, "SD" = 18, "PD" = 15, "NE" = 4),
  marker_color = NULL,
  marker_color_opt = NULL,
  anno_txt = anno_txt,
  xref_line = c(50, 100),
  xtick_at = waiver(),
  xlab = "Time from First Treatment (Day)",
  title = "Swimlane Plot"
)


# Example 2
library(dplyr)
library(nestcolor)

ADSL <- osprey::rADSL[1:20, ]
ADRS <- osprey::rADRS

anno_txt_vars <- c("ARMCD", "SEX", "COUNTRY")
anno_txt <- ADSL[, anno_txt_vars]

# markers from ADRS
ADRS <- dplyr::filter(ADRS, PARAMCD == "OVRINV") %>% select(USUBJID, ADY, AVALC)

# markers from ADSL - discontinuation
ADS <- ADSL %>%
  dplyr::filter(EOSSTT == "Discontinued" | DCSREAS != "") %>%
  select(USUBJID, EOSDY, DCSREAS) %>%
  dplyr::rename(ADY = EOSDY, AVALC = DCSREAS)

# combine ADRS with ADS records as one data for markers and join with ADSL
ANL <- inner_join(ADSL, rbind(ADRS, ADS), by = "USUBJID", multiple = "all")

g_swimlane(
  bar_id = sub(".*-", "", ADSL$USUBJID),
  bar_length = as.integer(ADSL$TRTEDTM - ADSL$TRTSDTM),
  sort_by = NULL,
  col_by = ADSL$ARMCD,
  marker_id = sub(".*-", "", ANL$USUBJID),
  marker_pos = ANL$ADY,
  marker_shape = ANL$AVALC,
  marker_shape_opt = c(
    "CR" = 16, "PR" = 17, "SD" = 18, "PD" = 15, "NE" = 0,
    "Adverse Event" = 7, "Death" = 8, "Physician Decision" = 9, "Progressive Disease" = 10,
    "Symptomatic Deterioation" = 11, "Withdrawal by Subject" = 12
  ),
  marker_color = ANL$AVALC,
  marker_color_opt = c(
    "CR" = "green", "PR" = "blue", "SD" = "yellow", "PD" = "red",
    "NE" = "grey", "Adverse Event" = "orange", "Death" = "black", "Physician Decision" = "navy",
    "Progressive Disease" = "purple", "Symptomatic Deterioation" = "cyan",
    "Withdrawal by Subject" = "darkred"
  ),
  anno_txt = anno_txt,
  xref_line = c(50, 100),
  xtick_at = waiver(),
  xlab = "Time from First Treatment (Day)",
  title = "Swimlane Plot"
)