We will here use the tabTOX and plotTOX
functions in the Data &
Functions page.
Download Tox_functions.R
# Data used
set.seed(1234)
n_AE <- 300
n_pat <- 100
df <- data.frame(OBS = sample(1:n_pat, n_AE, replace=T),
cat_tox = sample(paste("cat", 1:3), n_AE, replace=T),
tox = sample(paste("tox", 1:2), n_AE, replace=T),
tox_bis = sample(paste("tox", 1:20), n_AE, replace=T),
grade = sample(c(1, 2, 3, 4, 5, NA), n_AE, prob=c(0.3, 0.3, 0.2, 0.1, 0.05, 0.05), replace=T)) %>% arrange(OBS)
df$ARM <- ifelse(df$OBS%in%1:50, 'A', 'B')
df_bis <- data.frame(NAME = rep(paste("tox", 1:8), each=2),
N = sample(0:(n_pat/2), 16, replace=T),
ARM = rep(c('A', 'B'), 8))tabTOX function
tabae1 <- tabTOX(df, "OBS", var="tox", var_grade="grade",
grade_max=FALSE, percent="%", latex=FALSE, langue='en')| tox | N | N grade 1 | N grade 2 | N grade 3 | N grade 4 | N grade 5 | N missing grade |
|---|---|---|---|---|---|---|---|
| Total | 97 | 64 | 62 | 44 | 20 | 7 | 12 |
| tox 1 | 85 | 40 | 45 | 26 | 12 | 5 | 5 |
| tox 2 | 76 | 40 | 30 | 23 | 11 | 2 | 7 |
Here is another example where other optional parameters are used:
tabae2 <- tabTOX(df, "OBS", var="tox", var_cat="cat_tox", var_grade="grade",
grade_max=TRUE, percent="%", latex=FALSE, langue='en',
all=FALSE, addNA=FALSE, var_name="AE", total="All", n=n_pat)| AE | N grade 1 | N grade 2 | N grade 3 | N grade 4 | N grade 5 |
|---|---|---|---|---|---|
| All | 11 (11%) | 28 (28%) | 31 (31%) | 20 (20%) | 7 (7%) |
| cat 3 | 20 (20%) | 22 (22%) | 13 (13%) | 11 (11%) | 3 (3%) |
| - tox 1 | 16 (16%) | 17 (17%) | 10 (10%) | 7 (7%) | 1 (1%) |
| - tox 2 | 18 (18%) | 10 (10%) | 3 (3%) | 4 (4%) | 2 (2%) |
| cat 2 | 13 (13%) | 20 (20%) | 16 (16%) | 7 (7%) | 3 (3%) |
| - tox 1 | 10 (10%) | 14 (14%) | 8 (8%) | 2 (2%) | 3 (3%) |
| - tox 2 | 10 (10%) | 9 (9%) | 11 (11%) | 5 (5%) | 0 |
| cat 1 | 13 (13%) | 17 (17%) | 15 (15%) | 5 (5%) | 1 (1%) |
| - tox 2 | 11 (11%) | 10 (10%) | 10 (10%) | 3 (3%) | 0 |
| - tox 1 | 9 (9%) | 9 (9%) | 7 (7%) | 3 (3%) | 1 (1%) |
In the example above, only the maximal grade per toxicity is taken into account, missing grades and any grades are not displayed. Category of each adverse event is added. The percentages of the numbers are also displayed (per patients).
plotTOX function
Here is an example of adverse events visualization for two groups comparison without the optional arguments:
tabae3 <- plotTOX(baz=df, id="OBS", var="tox_bis",
n=c(n_pat/2,n_pat/2), arm="ARM", langue="en")
tabae3$plot
We can:
- Suppress toxicity for which both groups have a percentage less than 15% and add arrow for directional difference
tabae4 <- plotTOX(baz=df, id="OBS", var="tox_bis",
n=c(n_pat/2,n_pat/2), arm="ARM", langue="en",
percent_supp=15, favors=c("Favor B", "Favor A"),
y_favors_arrow=-0.1, y_favors_text=-0.3)
tabae4$plot
- Give directly a dataframe with three variables (in data frame
df_bis,NAMEindicates the type of toxicity,Nthe number of patients affected by the toxicity and the last one the randomization arm for which name can be given in the argumentarmof the function)
tabae5 <- plotTOX(baz=df_bis, id="OBS", var="tox_bis",
n=c(n_pat/2,n_pat/2), arm="ARM", langue="en",
y_favors_arrow=0, y_favors_text=-0.1)
tabae5$plot