Patient Profile Plot

Patient profile plot provides detailed information for a specific subject participating in the study. The plot includes relevant data for one subject that can help correlate adverse events, response, concomitant medications, exposure, and laboratory. The plotting of patient profile is modularized, with each domain plot generated by function patient_domain_profile. This g_patient_profile function assembles all requested domain plots into one patient profile. ADSL, ADEX, ADAE, ADRS, ADCM and ADLB data must be provided. The plot output will not include domains with data unspecified

Usage

g_patient_profile(
  ex = NULL,
  ae = NULL,
  rs = NULL,
  cm = NULL,
  lb = NULL,
  arrow_end_day,
  xlim = c(-28, 365),
  xlab = "Study Day",
  title = "Patient Profile"
)

Arguments

ex

list may contain

data dataframe for ADEX domain dataset
var vector to identify each lane of ADEX domain plot

ae

list may contain

data dataframe for ADAE domain dataset
var vector to identify each lane of ADAE plot
line_col factor vector to specify color for segments of ADAE plot
line_col_legend string to be displayed as line color legend title of ADAE plot
line_col_opt aesthetic values to map line color values of ADAE plot (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 ggplot default, please note that NULL needs to be specified

rs

list may contain

data dataframe for ADRS domain dataset
var vector to identify each lane of ADRS domain plot

cm

list may contain

data dataframe for ADCM domain dataset
var vector to identify each lane of ADCM domain plot

lb

list may contain

data dataframe for ADLB domain dataset
var vector to identify each lane of ADLB domain plot

arrow_end_day

numeric value indicates the end of arrow when arrows are requested

xlim

numeric vector for x-axis limit that will be shared by all domain plots, default is xlim = c(-28, 365)

xlab

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

title

string to be shown as title of the plot, default is "Patient Profile"

Value

plot object

Author

Xuefeng Hou (houx14) houx14@gene.com

Molly He (hey59) hey59@gene.com

Ting Qi (qit3) qit3@gene.com

Examples

library(scda)
library(dplyr)
library(nestcolor)

cached_data <- synthetic_cdisc_data("latest")

# ADSL
rADSL <- cached_data$adsl
ADSL <- rADSL %>%
  filter(USUBJID == rADSL$USUBJID[1]) %>%
  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)


# ADEX
rADEX <- cached_data$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
  ))

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

# ADRS
rADRS <- cached_data$adrs
ADRS <- rADRS %>%
  select(USUBJID, STUDYID, PARAMCD, PARAM, AVALC, AVAL, ADY, ADTM)
ADRS <- left_join(ADSL, ADRS, by = c("USUBJID", "STUDYID"))

# ADCM
rADCM <- cached_data$adcm
ADCM <- rADCM %>%
  select(USUBJID, STUDYID, ASTDTM, AENDTM, CMDECOD, ASTDY, AENDY)
ADCM <- left_join(ADSL, ADCM, by = c("USUBJID", "STUDYID"))

# ADLB
rADLB <- cached_data$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")))

# Example Patient Profile plot 5 domains
g_patient_profile(
  ex = list(
    data = ADEX,
    var = ADEX$PARCAT2
  ),
  ae = list(
    data = ADAE,
    var = ADAE$AEDECOD,
    line_col = factor(ADAE$AESER),
    line_col_legend = "Serious",
    line_col_opt = c("Y" = "red", "N" = "blue")
  ),
  rs = list(
    data = ADRS,
    var = ADRS$PARAMCD
  ),
  cm = list(
    data = ADCM,
    var = ADCM$CMDECOD
  ),
  lb = list(
    data = ADLB,
    var = ADLB$LBTESTCD
  ),
  arrow_end_day = ADSL$max_day,
  xlim = c(-28, ADSL$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.
#> Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.


# Example Patient Profile plot without ADCM and ADLB
g_patient_profile(
  ex = list(
    data = ADEX,
    var = ADEX$PARCAT2
  ),
  ae = list(
    data = ADAE,
    var = ADAE$AEDECOD,
    line_col = factor(ADAE$AESER),
    line_col_legend = "Serious",
    line_col_opt = c("Y" = "red", "N" = "blue")
  ),
  rs = list(
    data = ADRS,
    var = ADRS$PARAMCD
  ),
  arrow_end_day = ADSL$max_day,
  xlim = c(-28, ADSL$max_day),
  xlab = "Study Day",
  title = paste("Patient Profile: ", ADSL$USUBJID)
)
#> Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> = "none")` instead.

Usage

Arguments

Value

See also

Author

Examples