Creates Figures of Individual Observations from PKNCA Result
Source:R/NCA_Server.R
mk_figure_ind_obs.Rd
Takes the output of PKNCA and creates ggplot
figures faceted
by subject id highlighting of certain NCA aspects (e.g. points used for half-life)
Usage
mk_figure_ind_obs(
nca_res,
OBS_LAB = "Concentration ===CONCUNITS===",
TIME_LAB = "Time ===TIMEUNITS===",
OBS_STRING = "Observation",
BLQ_STRING = "BLQ",
NA_STRING = "Missing",
log_scale = TRUE,
scales = "fixed",
nfrows = 4,
nfcols = 3
)
Arguments
- nca_res
Output of PKNCA.
- OBS_LAB
Label of the observation axis with optional ===CONCUNITS=== placeholder for units.
- TIME_LAB
Label of the time axis with optional ===TIMEUNITS=== placeholder for units.
- OBS_STRING
Label for observation data.
- BLQ_STRING
Label for BLQ data.
- NA_STRING
Label for missing data.
- log_scale
Boolean variable to control y-scale (
TRUE
: Log 10,FALSE
: linear).- scales
String to determine the scales used when faceting. Can be either
"fixed"
,"free"
,"free_x"
, or"free_y"
.- nfrows
Number of facet rows per page.
- nfcols
Number of facet cols per page.
Value
List containing the element figures
which is a list of figure
pages ("Figure 1"
, "Figure 2"
, etc.). Each of these is
a also a list containing two elements:
gg: A ggplot object for that page.
notes: Placeholder for future notes, but NULL now.
Examples
# We need a state variable to be define
sess_res = NCA_test_mksession()
#> → ASM: including file
#> → ASM: source: file.path(system.file(package="onbrand"), "templates", "report.docx")
#> → ASM: dest: file.path("config","report.docx")
#> → ASM: including file
#> → ASM: source: file.path(system.file(package="onbrand"), "templates", "report.pptx")
#> → ASM: dest: file.path("config","report.pptx")
#> → ASM: including file
#> → ASM: source: file.path(system.file(package="onbrand"), "templates", "report.yaml")
#> → ASM: dest: file.path("config","report.yaml")
#> → ASM: State initialized
#> → ASM: module isgood: TRUE
#> → UD: including file
#> → UD: source: file.path(system.file(package="onbrand"), "templates", "report.docx")
#> → UD: dest: file.path("config","report.docx")
#> → UD: including file
#> → UD: source: file.path(system.file(package="onbrand"), "templates", "report.pptx")
#> → UD: dest: file.path("config","report.pptx")
#> → UD: including file
#> → UD: source: file.path(system.file(package="onbrand"), "templates", "report.yaml")
#> → UD: dest: file.path("config","report.yaml")
#> → UD: State initialized
#> → UD: module checksum updated:897d952fecbc804999396a96f9df4b20
#> → UD: module isgood: TRUE
#> → DW: including file
#> → DW: source: file.path(system.file(package="onbrand"), "templates", "report.docx")
#> → DW: dest: file.path("config","report.docx")
#> → DW: including file
#> → DW: source: file.path(system.file(package="onbrand"), "templates", "report.pptx")
#> → DW: dest: file.path("config","report.pptx")
#> → DW: including file
#> → DW: source: file.path(system.file(package="onbrand"), "templates", "report.yaml")
#> → DW: dest: file.path("config","report.yaml")
#> → DW: State initialized
#> → DW: module checksum updated:5b0f0b05ee3ac7336a74c564bb6efdad
#> → DW: loading data view idx: 1
#> → DW: setting name: Observations
#> → DW: module checksum updated:1ac3e0afcc601f848943f92b854b3830
#> → DW: -> filter
#> → DW: module checksum updated:67aff6e926eba73b3ecb361d26624844
#> → DW: -> filter
#> → DW: module checksum updated:0234f6d458ef7487a3b2e991b2d0957b
#> → DW: -> mutate
#> → DW: module checksum updated:37d0958f042076b974fdd3f894157822
#> → DW: loading data view idx: 2
#> → DW: setting name: PK 3mg SD IV
#> → DW: module checksum updated:4e7ca05728d66df3adfcf87387f9543a
#> → DW: -> filter
#> → DW: module checksum updated:2d95bc56262f46b7f135dd33fc4722b3
#> → DW: -> filter
#> → DW: module checksum updated:b8a30837145926d2d9cc6f788c10b7ed
#> → DW: -> filter
#> → DW: module checksum updated:24b554ee8736ebc84979c896ac2e93c3
#> → DW: -> filter
#> → DW: module checksum updated:daad88263faf7cbf90871ed00a0dd275
#> → DW: loading data view idx: 3
#> → DW: setting name: PK 3mg SD IV (NCA)
#> → DW: module checksum updated:a7b3ea35cdba272682716aa4619d3983
#> → DW: -> filter
#> → DW: module checksum updated:e8d2f77c0bd731995d845ee8be623e22
#> → DW: -> filter
#> → DW: module checksum updated:24cc7b591ca756a0abf560fb5295e04d
#> → DW: -> filter
#> → DW: module checksum updated:f79ef26bdb4dac420c24650b9e96f721
#> → DW: loading data view idx: 4
#> → DW: setting name: PKPD 3mg SD IV (NCA)
#> → DW: module checksum updated:c737e8b3a28ba600a83ddf58a969c90a
#> → DW: -> filter
#> → DW: module checksum updated:4c0d054f8ec47ae97fd1c650d8ddad55
#> → DW: -> filter
#> → DW: module checksum updated:1e3d65ec1bd6ee5850d67bd2250e3223
#> → DW: -> filter
#> → DW: module checksum updated:1e3d65ec1bd6ee5850d67bd2250e3223
#> → DW: module isgood: TRUE
#> → NCA: including file
#> → NCA: source: file.path(system.file(package="onbrand"), "templates", "report.docx")
#> → NCA: dest: file.path("config","report.docx")
#> → NCA: including file
#> → NCA: source: file.path(system.file(package="onbrand"), "templates", "report.pptx")
#> → NCA: dest: file.path("config","report.pptx")
#> → NCA: including file
#> → NCA: source: file.path(system.file(package="onbrand"), "templates", "report.yaml")
#> → NCA: dest: file.path("config","report.yaml")
#> ✖ NCA: Parameter specified in YAML is not a valid PKNCA parameter: sparse_se
#> ✖ NCA: Parameter specified in YAML is not a valid PKNCA parameter: sparse_df
#> → NCA: including file
#> → NCA: source: file.path(system.file(package="onbrand"), "templates", "report.docx")
#> → NCA: dest: file.path("config","report.docx")
#> → NCA: including file
#> → NCA: source: file.path(system.file(package="onbrand"), "templates", "report.pptx")
#> → NCA: dest: file.path("config","report.pptx")
#> → NCA: including file
#> → NCA: source: file.path(system.file(package="onbrand"), "templates", "report.yaml")
#> → NCA: dest: file.path("config","report.yaml")
#> → NCA: State initialized
#> → NCA: State initialized
#> → NCA: loading element idx: 1
#> → NCA: -> setting name: PK Example
#> → NCA: -> notes found and set
#> → NCA: -> setting data source: DW_myDS_3
#> → NCA: NCA_add_int: append
#> → NCA: NCA_add_int: append
#> → NCA: added element idx: 1
#> → NCA: loading element idx: 2
#> → NCA: -> setting name: PK/PD Example
#> → NCA: -> notes found and set
#> → NCA: -> setting data source: DW_myDS_4
#> → NCA: NCA_add_int: append
#> → NCA: NCA_add_int: append
#> → NCA: added element idx: 2
#> → NCA: module isgood: TRUE
state = sess_res$state
# Pulls out the active analysis
current_ana = NCA_fetch_current_ana(state)
# This is the raw PKNCA output
pknca_res = NCA_fetch_ana_pknca(state, current_ana)
# Building the figure
mk_res = mk_figure_ind_obs(nca_res = pknca_res)
mk_res$figures$Figure_1$gg