ggquickeda (version 0.3.3)

gglogisticexpdist: Create a logistic fit vs exposure(s)plot replaced by ggresponseexpdist

Description

Produces a logistic fit plot with a facettable exposures/quantiles/distributions in ggplot2

Usage

gglogisticexpdist(
  data = effICGI,
  response = "response",
  endpoint = "Endpoint",
  model_type = c("logistic"),
  DOSE = "DOSE",
  color_fill = "DOSE",
  logistic_by_color_fill = FALSE,
  exposure_metrics = c("AUC", "CMAX"),
  exposure_metric_split = c("median", "tertile", "quartile", "none"),
  exposure_metric_soc_value = -99,
  exposure_metric_plac_value = 0,
  exposure_distribution = c("distributions", "lineranges", "boxplots", "none"),
  exposure_distribution_percent = TRUE,
  exposure_distribution_percent_text_size = 5,
  dose_plac_value = "Placebo",
  xlab = "Exposure Values",
  ylab = "Probability of Response",
  points_alpha = 0.2,
  points_show = TRUE,
  prob_obs_byexptile = TRUE,
  prob_obs_byexptile_plac = TRUE,
  prob_obs_byexptile_group = "none",
  prob_text_size = 5,
  prob_obs_bydose = TRUE,
  prob_obs_bydose_plac = FALSE,
  Nresp_Ntot_show = TRUE,
  Nresp_Ntot_size = 5,
  Nresp_Ntot_ypos = c("with percentages", "top"),
  Nresp_Ntot_sep = "/",
  binlimits_show = TRUE,
  binlimits_text_size = 5,
  binlimits_ypos = 0,
  binlimits_color = "#B3B3B380",
  dist_position_scaler = 0.2,
  dist_offset = 0,
  dist_scale = 0.9,
  lineranges_ypos = 0.2,
  lineranges_dodge = 0.15,
  lineranges_doselabel = FALSE,
  proj_bydose = TRUE,
  yproj = TRUE,
  yproj_xpos = 0,
  yproj_dodge = 0.2,
  yaxis_position = c("left", "right"),
  facet_formula = NULL,
  theme_certara = TRUE,
  return_list = FALSE
)

Arguments

data

Data to use with multiple endpoints stacked into response (values), Endpoint(endpoint name)

response

name of the column holding the response values

endpoint

name of the column holding the name/key of the endpoint default to Endpoint

model_type

type of the trend fit one of "logistic", "none"

DOSE

name of the column holding the DOSE values default to DOSE

color_fill

name of the column to be used for color/fill default to DOSE column

logistic_by_color_fill

fit split by color? default FALSE

exposure_metrics

name(s) of the column(s) to be stacked into expname exptile and split into exposure_metric_split

exposure_metric_split

one of "median", "tertile", "quartile", "none"

exposure_metric_soc_value

special exposure code for standard of care default -99

exposure_metric_plac_value

special exposure code for placebo default 0

exposure_distribution

one of distributions, lineranges, boxplots or none

exposure_distribution_percent

show percent of distribution between binlimits TRUE/FALSE

exposure_distribution_percent_text_size

distribution percentages text size default to 5

dose_plac_value

string identifying placebo in DOSE column

xlab

text to be used as x axis label

ylab

text to be used as y axis label

points_alpha

alpha transparency for points

points_show

show the observations TRUE/FALSE

prob_obs_byexptile

observed probability by exptile TRUE/FALSE

prob_obs_byexptile_plac

observed probability by exptile placebo TRUE/FALSE

prob_obs_byexptile_group

additional grouping for exptile probabilities default none

prob_text_size

probability text size default to 5

prob_obs_bydose

observed probability by dose TRUE/FALSE

prob_obs_bydose_plac

observed probability by placebo dose TRUE/FALSE

Nresp_Ntot_show

show N responders/Ntotal ? TRUE/FALSE

Nresp_Ntot_size

N responders/Ntotal text size default to 5

Nresp_Ntot_ypos

y position for N responders/Ntotal two text elements the first for by exptile and the second for by dose/color options include with percentages top bottom

Nresp_Ntot_sep

character string to separate N responders/ Ntotal default /

binlimits_show

show the binlimits vertical lines TRUE/FALSE

binlimits_text_size

binlimits text size default to 5

binlimits_ypos

binlimits y position default to 0

binlimits_color

binlimits text color default to alpha("gray70",0.5)

dist_position_scaler

space occupied by the distribution default to 0.2

dist_offset

offset where the distribution position starts default to 0

dist_scale

scaling parameter for ggridges default to 0.9

lineranges_ypos

where to put the lineranges -1

lineranges_dodge

lineranges vertical dodge value 1

lineranges_doselabel

TRUE/FALSE

proj_bydose

project the probabilities on logistic curve TRUE/FALSE

yproj

project the probabilities on y axis TRUE/FALSE

yproj_xpos

y projection x position 0

yproj_dodge

y projection dodge value 0.2

yaxis_position

where to put y axis "left" or "right"

facet_formula

facet formula to be use otherwise endpoint ~ expname

theme_certara

apply certara colors and format for strips and default colour/fill

return_list

What to return if True a list of the datasets and plot is returned instead of only the plot

Examples

if (FALSE) {
# Example 1
library(ggplot2)
effICGI <- logistic_data |>
dplyr::filter(!is.na(ICGI))|>
dplyr::filter(!is.na(AUC))
effICGI$DOSE <- factor(effICGI$DOSE,
                      levels=c("0", "600", "1200","1800","2400"),
                      labels=c("Placebo", "600 mg", "1200 mg","1800 mg","2400 mg"))
effICGI$STUDY <- factor(effICGI$STUDY)    
effICGI$ICGI2 <- effICGI$ICGI
effICGI <- tidyr::gather(effICGI,Endpoint,response,ICGI,ICGI2)
gglogisticexpdist(data = effICGI |>
                 dplyr::filter(Endpoint=="ICGI"),
                 response = "response",
                 endpoint = "Endpoint",
                 exposure_metrics = c("AUC"),
                 exposure_metric_split = c("quartile"),
                 exposure_metric_soc_value = -99,
                 exposure_metric_plac_value = 0,
                 exposure_distribution ="distributions",
                 yproj_xpos = -15,
                 yproj_dodge = 10,
                 dist_position_scaler = 0.1,
                 dist_offset = -0.1,
                 Nresp_Ntot_ypos = c("with percentages","bottom"),
                 prob_obs_bydose_plac = TRUE,
                 prob_obs_byexptile_plac = FALSE,
                 prob_obs_byexptile_group = "none",
                 binlimits_ypos = 0.3,
                 binlimits_color = "#475c6b",
                 points_alpha= 0.8)
                 
# Example 2                
gglogisticexpdist(data = effICGI |>
                 dplyr::filter(Endpoint=="ICGI"),
                 response = "response",
                 endpoint = "Endpoint",
                 exposure_metrics = c("CMAX"),
                 exposure_metric_split = c("tertile"),
                 exposure_metric_soc_value = -99,
                 exposure_metric_plac_value = 0,
                 exposure_distribution ="lineranges",
                 lineranges_ypos = -0.2,
                 lineranges_dodge = 0.2,
                 lineranges_doselabel = TRUE,
                 Nresp_Ntot_ypos = c("with percentages","bottom"),
                 prob_obs_bydose_plac = TRUE,
                 prob_obs_byexptile_plac = FALSE,
                 prob_obs_byexptile_group = "none",yproj_xpos = -1,
                 yproj_dodge = 2,
                 binlimits_color = "#475c6b",
                 dist_position_scaler = 0.1)
                 
#' # Example 3                
library(ggh4x)
gglogisticexpdist(data = effICGI |>
                 dplyr::filter(Endpoint=="ICGI"), 
                 response = "response",
                 endpoint = "Endpoint",
                 DOSE = "DOSE",
                 exposure_metrics = c("AUC"),
                 exposure_metric_split = c("quartile"),
                 exposure_distribution ="distributions",
                 exposure_metric_soc_value = -99,
                 exposure_metric_plac_value = 0,
                 dist_position_scaler = 0.15)+
 facet_grid2(Endpoint~expname+DOSE2,scales="free",
 margins = "DOSE2",strip = strip_nested())
# Example 4  
effICGI$SEX <- as.factor(effICGI$SEX)               
gglogisticexpdist(data = effICGI  |>
                 dplyr::filter(Endpoint=="ICGI"), 
                 response = "response",
                 endpoint = "Endpoint",
                 DOSE = "DOSE",
                 color_fill = "SEX",
                 exposure_metrics = c("AUC"),
                 exposure_metric_split = c("quartile"),
                 exposure_distribution ="distributions",
                 exposure_metric_soc_value = -99,
                 exposure_metric_plac_value = 0,
                 lineranges_ypos = -0.2,
                 yproj_xpos = -10,
                 yproj_dodge = 20,
                 prob_text_size = 6,
                 binlimits_text_size = 6,
                 Nresp_Ntot_show = TRUE,
                 dist_position_scaler = 0.15)+
                 ggplot2::scale_x_continuous(breaks = seq(0,350,50),
                 expand = ggplot2::expansion(add= c(0,0),mult=c(0,0)))+
                 ggplot2::coord_cartesian(xlim = c(-30,355))+
                 ggplot2::facet_grid(Endpoint~expname+color_fill2, margins ="color_fill2" )

#Example 4b
  effICGI$SEX <- as.factor(effICGI$SEX)
 gglogisticexpdist(data = effICGI |>
  dplyr::filter(Endpoint =="ICGI"),
                 response = "response",
                 endpoint = "Endpoint",
                 color_fill = "SEX",
                 exposure_metrics = c("AUC"),
                 exposure_metric_split = c("quartile"),
                 exposure_metric_soc_value = -99,
                 exposure_metric_plac_value = 0,
                 dist_position_scaler = 1, dist_offset = -1 ,
                 yproj_xpos =  -20 ,
                 yproj_dodge = 20 ,
                 exposure_distribution ="lineranges",
                 lineranges_doselabel = TRUE)
                 
#Example 5
gglogisticexpdist(data = effICGI |> dplyr::filter(Endpoint=="ICGI"), 
                  response = "response",
                  endpoint = "Endpoint",
                  DOSE = "DOSE",
                  exposure_metrics = c("AUC"),
                  exposure_metric_split = c("quartile"),
                  exposure_distribution ="distributions",
                  exposure_metric_soc_value = -99,
                  exposure_metric_plac_value = 0,
                  dist_position_scaler = 0.15)+
                 facet_grid(Endpoint~expname+exptile,scales="free",
                 margins = "exptile")
#Example 6
a <- gglogisticexpdist(data = effICGI, # 
                  response = "response",
                  endpoint = "Endpoint",
                  DOSE = "DOSE",yproj_dodge = 36,
                  exposure_metrics = c("AUC"),
                  exposure_metric_split = c("quartile"),
                  exposure_distribution ="lineranges",
                  exposure_metric_soc_value = -99,
                  exposure_metric_plac_value = 0) +
  facet_grid(Endpoint~expname,switch = "both")
b <-   gglogisticexpdist(data = effICGI, # 
                    response = "response",
                    endpoint = "Endpoint",
                    DOSE = "DOSE",yproj_dodge = 2,
                    exposure_metrics = c("CMAX"),
                    exposure_metric_split = c("quartile"),
                    exposure_distribution ="lineranges",
                    exposure_metric_soc_value = -99,
                    exposure_metric_plac_value = 0,
                    yaxis_position = "right")+
  facet_grid(Endpoint~expname,switch = "x")+
  theme(strip.text.y.right = element_blank(),
        strip.background.y = element_blank())
library(patchwork)
(a | b ) +
  plot_layout(guides = "collect", axes = "collect_x")&
  theme(legend.position = "top")

#Example 7
effICGI <- logistic_data |>
dplyr::filter(!is.na(ICGI))|>
dplyr::filter(!is.na(AUC))
effICGI$DOSE <- factor(effICGI$DOSE,
                      levels=c("0", "600", "1200","1800","2400"),
                      labels=c("Placebo", "600 mg", "1200 mg","1800 mg","2400 mg"))
effICGI$STUDY <- factor(effICGI$STUDY)
effICGI$ICGI2 <- ifelse(effICGI$ICGI7 < 4,1,0)
effICGI$ICGI3 <- ifelse(effICGI$ICGI7 < 5,1,0)

effICGI <- tidyr::gather(effICGI,Endpoint,response,ICGI,ICGI2,ICGI3)
effICGI$endpointcol2 <- effICGI$Endpoint
effICGI$endpointcol3 <- effICGI$Endpoint
gglogisticexpdist(data = effICGI,
                  response = "response",
                 endpoint = "Endpoint",
                  exposure_metrics = c("AUC"),
                  exposure_metric_split = c("tertile"),
                  exposure_metric_soc_value = -99,
                  exposure_metric_plac_value = 0,
                  color_fill = "endpointcol2",                   
                  logistic_by_color_fill = TRUE,
                  Nresp_Ntot_show = TRUE,
                  Nresp_Ntot_ypos = c("with percentages","bottom"),
                  prob_obs_byexptile = FALSE,
                  prob_obs_byexptile_group="endpointcol3",
                  prob_obs_byexptile_plac = FALSE,
                  prob_obs_bydose_plac = TRUE,
                  binlimits_color = "#475c6b",
                  exposure_distribution ="distributions",
                  prob_obs_bydose = TRUE,
                  proj_bydose = FALSE,
                  yproj = FALSE,
                  dist_position_scaler = 0.1,
                  dist_offset = -0.1)+
  facet_grid(expname~Endpoint,scales="free_x")
#Example 8  
gglogisticexpdist(data = effICGI,
                  response = "response",
                 endpoint = "endpointcol2",
                  exposure_metrics = c("AUC"),
                  exposure_metric_split = c("quartile"),
                  exposure_metric_soc_value = -99,
                  exposure_metric_plac_value = 0,
                  color_fill = "Endpoint",                   
                  logistic_by_color_fill = TRUE,
                  Nresp_Ntot_show = FALSE, points_show = FALSE,
                  prob_obs_byexptile = TRUE,
                  prob_obs_byexptile_group="endpointcol3",
                  prob_obs_byexptile_plac = TRUE,
                  prob_obs_bydose = FALSE,
                  prob_obs_bydose_plac = FALSE,
                  binlimits_color = "#475c6b",
                  exposure_distribution ="distributions",
                  proj_bydose = FALSE,
                  yproj = FALSE,
                  dist_position_scaler = 0.1,
                  dist_offset = -0.1)+
  facet_grid(expname~.,scales="free_x")
}