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Patient Domain Profile

Source: R/g_patient_profile.R
patient_domain_profile.Rd

Patient domain profile provides information for a specific subject that participated in the study. The plot includes relevant data for one subject in a user specified domain, including adverse events (ADAE), response (ADRS), concomitant medications (ADCM), exposure (ADEX), and laboratory (ADLB).

Usage

patient_domain_profile(
  domain = NULL,
  var_names,
  marker_pos,
  arrow_end,
  xtick_at = waiver(),
  line_col_list = NULL,
  line_width = 1,
  arrow_size = 0.1,
  no_enddate_extention = 0,
  marker_col_list = NULL,
  marker_shape_list = NULL,
  show_days_label = TRUE,
  xlim = c(-28, max(marker_pos) + 5),
  xlab = NULL,
  show_title = TRUE,
  title = NULL
)

Arguments

domain

string of domain name to be shown as y-axis label, default is NULL (no y-axis label shown)

var_names

character vector to identify each lane

marker_pos

Depending on the domain, this can be

  • marker position numeric vector for domains ADEX, ADLB, and ADRS

  • numeric data frame with two columns, start and end time marker position, for domains ADAE and ADCM

arrow_end

numeric value indicates the end of arrow when arrows are requested

xtick_at

numeric vector with the locations of the x-axis tick marks

line_col_list

a list may contain

  • line_col: factor vector to specify color for segments , default is NULL (no line color is specified)

  • line_col_opt aesthetic values to map color values (named vector to map color values to each name). If not NULL, please make sure this contains all possible values for line_col values, otherwise color will be assigned by hcl.colors

  • line_col_legend: a string to be displayed as line color legend title when line_col is specified, default is NULL (no legend title is displayed)

line_width

numeric value for segment width, default is line_width = 1

arrow_size

numeric value for arrow size, default is arrow_size = 0.1

no_enddate_extention

numeric value for extending the arrow when end date is missing for ADAE or ADCM domain. Default is no_enddate_extention = 0.

marker_col_list

a list may contain

  • marker_col a factor vector to specify color for markers, default is NULL (no color markers is specified)

  • marker_col_opt aesthetic values to map color values (named vector to map color values to each name) If not NULL, please make sure this contains all possible values for marker_col values, otherwise color will be assigned by hcl.colors

  • marker_col_legend a string to be displayed as marker color legend title, default is NULL (no legend title is displayed)

marker_shape_list

a list may contain

  • marker_shape factor vector to specify shape for markers, default is NULL (no shape marker is specified)

  • marker_shape_opt aesthetic values to map shape values (named vector to map shape values to each name). If not NULL, please make sure this contains all possible values for marker_shape values, otherwise shape will be assigned by ggplot default

  • marker_shape_legend string to be displayed as marker shape legend title, default is NULL (no legend title is displayed)

show_days_label

boolean value for showing y-axis label, default is TRUE

xlim

numeric vector for x-axis limit, default is xlim = c(-28, max(marker_pos) + 5)

xlab

string to be shown as x-axis label, default is "Study Day"

show_title

boolean value for showing title of the plot, default is TRUE

title

string to be shown as title of the plot, default is NULL (no plot title is displayed)

Value

plot object

Author

Xuefeng Hou (houx14) houx14@gene.com

Tina Cho (chot) tina.cho@roche.com

Molly He (hey59) hey59@gene.com

Ting Qi (qit3) qit3@gene.com

Examples

library(scda)
library(dplyr)

# ADSL
rADSL <- synthetic_cdisc_data("latest")$adsl
ADSL <- rADSL %>%
  group_by(USUBJID) %>%
  mutate(
    TRTSDT = as.Date(TRTSDTM),
    max_date = max(as.Date(LSTALVDT), as.Date(DTHDT), na.rm = TRUE),
    max_day = as.numeric(as.Date(max_date) - as.Date(TRTSDT)) + 1
  ) %>%
  select(USUBJID, STUDYID, TRTSDT, max_day) %>%
  filter(USUBJID == rADSL$USUBJID[1])
#> Warning: no non-missing arguments to max; returning -Inf
#> Warning: no non-missing arguments to max; returning -Inf
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# Example 1 Exposure "ADEX"
rADEX <- synthetic_cdisc_data("latest")$adex
ADEX <- rADEX %>%
  select(USUBJID, STUDYID, ASTDTM, PARCAT2, AVAL, AVALU, PARAMCD)
ADEX <- left_join(ADSL, ADEX, by = c("USUBJID", "STUDYID"))
ADEX <- ADEX %>%
  filter(PARAMCD == "DOSE") %>%
  arrange(PARCAT2, PARAMCD) %>%
  mutate(diff = c(0, diff(AVAL, lag = 1))) %>%
  mutate(
    Modification = case_when(
      diff < 0 ~ "Decrease",
      diff > 0 ~ "Increase",
      diff == 0 ~ "None"
    )
  ) %>%
  mutate(
    ASTDT_dur = as.numeric(
      as.Date(
        substr(as.character(ASTDTM), 1, 10)
      ) - as.Date(TRTSDT) + 1
    )
  )

p1 <- patient_domain_profile(
  domain = "Exposure (ADEX)",
  var_names = ADEX$PARCAT2,
  marker_pos = ADEX$ASTDT_dur,
  arrow_end = ADSL$max_day,
  xtick_at = waiver(),
  line_col_list = NULL,
  line_width = 1,
  arrow_size = 0.1,
  no_enddate_extention = 0,
  marker_col_list = list(
    marker_col = factor(ADEX$Modification),
    marker_col_opt = c("Increase" = "red", "Decrease" = "green", "None" = "blue"),
    marker_col_legend = NULL
  ),
  marker_shape_list = list(
    marker_shape = factor(ADEX$Modification),
    marker_shape_opt = c("Increase" = 24, "Decrease" = 25, "None" = 23),
    marker_shape_legend = "Dose Modification"
  ),
  show_days_label = TRUE,
  xlim = c(-28, ADSL$max_day),
  xlab = "Study Day",
  title = paste("Patient Profile: ", ADSL$USUBJID)
)
p1


# Example 2 Adverse Event "ADAE"
# Note that ASTDY is represented by a circle and AENDY is represented by a square.
# If AENDY and ASTDY occur on the same day only AENDY will be shown.

# Adverse Event ADAE
rADAE <- synthetic_cdisc_data("latest")$adae
ADAE <- rADAE %>%
  select(USUBJID, STUDYID, AESOC, AEDECOD, AESER, AETOXGR, AEREL, ASTDY, AENDY)
ADAE <- left_join(ADSL, ADAE, by = c("USUBJID", "STUDYID"))

p2 <- patient_domain_profile(
  domain = "Adverse Event (ADAE)",
  var_names = ADAE$AEDECOD,
  marker_pos = ADAE[, c("ASTDY", "AENDY")],
  arrow_end = ADSL$max_day,
  xtick_at = waiver(),
  line_col_list = list(
    line_col = ADAE$AESER,
    line_col_legend = "Serious",
    line_col_opt = c("blue", "green")
  ),
  line_width = 1,
  arrow_size = 0.1,
  no_enddate_extention = 0,
  marker_col_list = list(
    marker_col = factor(ADAE$AETOXGR),
    marker_col_opt = c("3" = "yellow", "4" = "red"),
    marker_col_legend = NULL
  ),
  marker_shape_list = list(
    marker_shape = NULL,
    marker_shape_opt = NULL,
    marker_shape_legend = "Grade"
  ),
  show_days_label = TRUE,
  xlim = c(-28, ADSL$max_day),
  xlab = "Study Day",
  title = paste("Patient Profile: ", ADSL$USUBJID)
)
#> Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
p2


# Example 3 Tumor Response "ADRS"
rADRS <- synthetic_cdisc_data("latest")$adrs
ADRS <- rADRS %>%
  select(USUBJID, STUDYID, PARAMCD, PARAM, AVALC, AVAL, ADY, ADTM)
ADRS <- left_join(ADSL, ADRS, by = c("USUBJID", "STUDYID"))
p3 <- patient_domain_profile(
  domain = "Tumor Response (ADRS)",
  var_names = ADRS$PARAMCD,
  marker_pos = ADRS$ADY,
  arrow_end = ADSL$max_day,
  xtick_at = waiver(),
  line_col_list = NULL,
  line_width = 1,
  arrow_size = 0.1,
  no_enddate_extention = 0,
  marker_col_list = list(
    marker_col = factor(ADRS$AVALC),
    marker_col_opt = c(
      "CR" = "green", "PR" = "blue",
      "SD" = "yellow", "PD" = "red", "NE" = "pink",
      "Y" = "lightblue", "N" = "darkred"
    ),
    marker_col_legend = NULL
  ),
  marker_shape_list = list(
    marker_shape = factor(ADRS$AVALC),
    marker_shape_opt = c(
      "CR" = 21, "PR" = 24,
      "SD" = 23, "PD" = 22, "NE" = 14,
      "Y" = 11, "N" = 8
    ),
    marker_shape_legend = "Response"
  ),
  show_days_label = TRUE,
  xlim = c(-28, ADSL$max_day),
  xlab = "Study Day",
  title = paste("Patient Profile: ", ADSL$USUBJID)
)
p3


# Example 4 Concomitant Med "ADCM"
rADCM <- synthetic_cdisc_data("latest")$adcm
ADCM <- rADCM %>%
  select(USUBJID, STUDYID, ASTDTM, AENDTM, CMDECOD, ASTDY, AENDY)
ADCM <- left_join(ADSL, ADCM, by = c("USUBJID", "STUDYID"))
p4 <- patient_domain_profile(
  domain = "Concomitant Med (ADCM)",
  var_names = ADCM$CMDECOD,
  marker_pos = ADCM[, c("ASTDY", "AENDY")],
  arrow_end = ADSL$max_day,
  xtick_at = waiver(),
  line_col_list = list(line_col_opt = "orange"),
  line_width = 1,
  arrow_size = 0.1,
  no_enddate_extention = 50,
  marker_col_list = list(marker_col_opt = "orange"),
  marker_shape_list = NULL,
  show_days_label = TRUE,
  xlim = c(-28, ADSL$max_day),
  xlab = "Study Day",
  title = paste("Patient Profile: ", ADSL$USUBJID)
)
#> Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
#> Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
#> Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.
p4


# Example 5 Laboratory "ADLB"
rADLB <- synthetic_cdisc_data("latest")$adlb
ADLB <- rADLB %>%
  select(
    USUBJID, STUDYID, LBSEQ, PARAMCD, BASETYPE,
    ADTM, ADY, ATPTN, AVISITN, LBTESTCD, ANRIND
  )
ADLB <- left_join(ADSL, ADLB, by = c("USUBJID", "STUDYID"))

ADLB <- ADLB %>%
  group_by(USUBJID) %>%
  mutate(ANRIND = factor(ANRIND, levels = c("LOW", "NORMAL", "HIGH")))

p5 <- patient_domain_profile(
  domain = "Laboratory (ADLB)",
  var_names = ADLB$LBTESTCD,
  marker_pos = ADLB$ADY,
  arrow_end = ADSL$max_day,
  xtick_at = waiver(),
  line_col_list = NULL,
  line_width = 1,
  arrow_size = 0.1,
  no_enddate_extention = 0,
  marker_col_list = list(
    marker_col = factor(ADLB$ANRIND),
    marker_col_opt = c(
      "HIGH" = "red", "LOW" = "blue",
      "NORMAL" = "green", "NA" = "green"
    )
  ),
  marker_shape_list = list(
    marker_shape = factor(ADLB$ANRIND),
    marker_shape_opt = c(
      "HIGH" = 24, "LOW" = 25,
      "NORMAL" = 23, "NA" = 23
    ),
    marker_shape_legend = "Labs Abnormality"
  ),
  show_days_label = TRUE,
  xlim = c(-30, ADSL$max_day),
  xlab = "Study Day",
  title = paste("Patient Profile: ", ADSL$USUBJID)
)
p5