Quality of life outcomes in a cancer trial: dealing with missing data
The EORTC QLQ-C30 is a 30-item questionnaire that has been designed for use in a wide range of cancer patient populations and is a reliable and valid measure of the quality of life in cancer patients. It includes a number of different scales, but this challenge is focussed on the global health and quality of life scale (QL).
A recording of the session can be found here.
Example 1.
Example 2.
Example 3.
Example 4.
Example 5.
Example 6.
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Code
Example 1.
library(dplyr)
library(tidyr)
library(ggplot2)
library(forcats)
library(scales)
d0 <- read.csv2("ww eortc qlq-c30 missing.csv", sep=",") %>%
as_tibble()
d0
d1 <- df %>%
pivot_longer(cols=starts_with("WEEK"), names_to = "AVISIT", values_to = "AVAL") %>%
mutate(AVAL=as.numeric(AVAL)) %>%
select(USUBJID, ARM, LASTVIS, AGE:AVAL)
d1
d2 <- d1 %>%
group_by(ARM, LASTVIS, AVISIT) %>%
summarize(AVAL = mean(AVAL, na.rm=TRUE)) %>%
mutate(LASTVISC=as.factor(paste("Week", sprintf("%02.f", LASTVIS))),
AVISITN = as.numeric(gsub("WEEK","",AVISIT))) %>%
mutate(LASTVISC=fct_reorder(LASTVISC, LASTVIS))
cc <- scales::seq_gradient_pal("yellow", "blue", "Lab")(seq(0,1,length.out=14))
show_col(cc)
breaks <- sort(names(table(df_2$LASTVISC)))
labels <- breaks
ggplot(data=d2, aes(x=AVISITN, y=AVAL, group=LASTVISC, color=LASTVISC)) +
geom_line() +
geom_point() +
scale_y_continuous(breaks = round(seq(0, 100, 8.333333333),2),
limits = c(0, 100)) +
scale_x_continuous(breaks = seq(0, 48, 3), labels = paste("Wk", seq(0, 48, 3))) +
scale_color_manual(values = cc, labels=labels, breaks=breaks) +
facet_grid(cols=vars(ARM)) +
labs(title = "Dropout is associated with worsening in quality of life",
y = "EORTC QLQ-C30 QL [0-100]",
x = "Week on treatment") +
theme(plot.background = element_rect(fill="black"),
panel.background = element_rect(fill="black"),
legend.background = element_rect(fill="black"),
legend.box.background = element_rect(fill="black"),
legend.key = element_blank(),
legend.text = element_text(colour="grey"),
panel.grid = element_line(colour="grey5"),
panel.grid.minor = element_blank(),
strip.background = element_blank(),
plot.title=element_text(colour = "grey", size = 14, face = "bold"),
strip.text = element_text(colour = "grey50", size = 10),
axis.text = element_text(angle = 90))
ggsave(filename = "line_plot.png", device = "png", width = 12, height = 6)
Example 2.
No code has been submitted.
Example 3.
No code has been submitted.
Example 4.
library(dplyr)
library(tidyr)
library(ggplot2)
library(forcats)
library(scales)
library(ggalluvial)
library(RColorBrewer)
df <- read.csv2("ww eortc qlq-c30 missing.csv", sep=",") %>%
as_tibble()
df
df_1 <- df %>%
pivot_longer(cols=starts_with("WEEK"), names_to = "AVISIT", values_to = "AVAL") %>%
select(USUBJID, ARM, LASTVIS, AGE:AVAL) %>%
mutate(AVAL=as.factor(if_else(AVAL=="", "Missing", AVAL)))
df_1
levels(df_1$AVAL) <- c(as.character(rev(round(seq(0, 100, 8.333333333), 1))), "Missing")
cc <- scales::div_gradient_pal(low = "#a50026", mid="#ffffbf", high = "#313695", "Lab")(seq(0,1,length.out=13))
colors <- c(cc, "#D3D3D3")
show_col(colors)
ggplot(df_1,
aes(
x = AVISIT,
stratum = AVAL,
alluvium = USUBJID,
fill = AVAL,
label = AVAL
)) +
scale_fill_manual(values = colors) +
scale_x_discrete(labels = paste("Wk", seq(0, 48, 3))) +
geom_flow(stat = "alluvium",
lode.guidance = "frontback",
color = "darkgray") +
geom_stratum() +
labs(title = "Quality of Life - Missing data depends on age and treatment received") +
facet_wrap(AGEGR~ARM, nrow = 4, scales = "free_y", strip.position = c("left")) +
# facet_grid(cols = vars(ARM), rows = vars(AGEGR), scales = "free") +
theme_bw() +
guides(fill = guide_legend(nrow = 1, reverse = T)) +
theme(
#panel.background = element_blank(),
#axis.text.y = element_blank(),
legend.title = element_blank(),
axis.title.x = element_blank(),
legend.position = "bottom",
strip.text = element_text(size = 12),
axis.text = element_text(angle = 90),
legend.direction = "horizontal"
)
ggsave(filename = "sankey_chart.png", device = "png", width = 16, height = 9)
Example 5.
No code has been submitted.
Example 6.
No code has been submitted.