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 forADEX
domain datasetvar
vector to identify each lane ofADEX
domain plot
- ae
list may contain
data
dataframe forADAE
domain datasetvar
vector to identify each lane ofADAE
plotline_col
factor vector to specify color for segments ofADAE
plotline_col_legend
string to be displayed as line color legend title ofADAE
plotline_col_opt
aesthetic values to map line color values ofADAE
plot (named vector to map color values to each name). If notNULL
, please make sure this contains all possible values forline_col
values, otherwise color will be assigned byggplot
default, please note thatNULL
needs to be specified
- rs
list may contain
data
dataframe forADRS
domain datasetvar
vector to identify each lane ofADRS
domain plot
- cm
list may contain
data
dataframe forADCM
domain datasetvar
vector to identify each lane ofADCM
domain plot
- lb
list may contain
data
dataframe forADLB
domain datasetvar
vector to identify each lane ofADLB
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"
Author
Xuefeng Hou (houx14) houx14@gene.com
Molly He (hey59) hey59@gene.com
Ting Qi (qit3) qit3@gene.com
Examples
library(dplyr)
library(nestcolor)
# ADSL
ADSL <- osprey::rADSL %>%
filter(USUBJID == rADSL$USUBJID[1]) %>%
mutate(
TRTSDT = as.Date(TRTSDTM),
max_date = max(as.Date(LSTALVDT), as.Date(DTHDT), na.rm = TRUE),
max_day = as.numeric(as.Date(max_date) - as.Date(TRTSDT)) + 1
) %>%
select(USUBJID, STUDYID, TRTSDT, max_day)
# ADEX
ADEX <- osprey::rADEX %>%
select(USUBJID, STUDYID, ASTDTM, PARCAT2, AVAL, AVALU, PARAMCD)
ADEX <- left_join(ADSL, ADEX, by = c("USUBJID", "STUDYID"))
ADEX <- ADEX %>%
filter(PARAMCD == "DOSE") %>%
arrange(PARCAT2, PARAMCD) %>%
mutate(diff = c(0, diff(AVAL, lag = 1))) %>%
mutate(Modification = case_when(
diff < 0 ~ "Decrease",
diff > 0 ~ "Increase",
diff == 0 ~ "None"
)) %>%
mutate(ASTDT_dur = as.numeric(
as.Date(substr(as.character(ASTDTM), 1, 10)) -
as.Date(TRTSDT) + 1
))
# ADAE
ADAE <- osprey::rADAE %>%
select(USUBJID, STUDYID, AESOC, AEDECOD, AESER, AETOXGR, AEREL, ASTDY, AENDY)
ADAE <- left_join(ADSL, ADAE, by = c("USUBJID", "STUDYID"))
# ADRS
ADRS <- osprey::rADRS %>%
select(USUBJID, STUDYID, PARAMCD, PARAM, AVALC, AVAL, ADY, ADTM)
ADRS <- left_join(ADSL, ADRS, by = c("USUBJID", "STUDYID"))
# ADCM
ADCM <- osprey::rADCM %>%
select(USUBJID, STUDYID, ASTDTM, AENDTM, CMDECOD, ASTDY, AENDY)
ADCM <- left_join(ADSL, ADCM, by = c("USUBJID", "STUDYID"))
# ADLB
ADLB <- osprey::rADLB %>%
select(
USUBJID, STUDYID, LBSEQ, PARAMCD, BASETYPE, ADTM,
ADY, ATPTN, AVISITN, LBTESTCD, ANRIND
)
ADLB <- left_join(ADSL, ADLB, by = c("USUBJID", "STUDYID"))
ADLB <- ADLB %>%
group_by(USUBJID) %>%
mutate(ANRIND = factor(ANRIND, levels = c("LOW", "NORMAL", "HIGH")))
# Example Patient Profile plot 5 domains
g_patient_profile(
ex = list(
data = ADEX,
var = ADEX$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)
)
# 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)
)