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fw_vw_1.R
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fw_vw_1.R
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# BIND DATA ---------------------------------------------------------------
common <- intersect(colnames(fluwatch),#cols from fluwatch
colnames(vw_pos))
s_list[["s.fw_vw_all"]] <- common %>%
setdiff(., c("illnessid", "individual_id", "nVar", "age3"))
fw_vw <- rbind(fluwatch %>% select(common),
vw_pos %>% select(common)) %>%
mutate(across(s_list[["s.fw_vw_all"]], ~ifelse(is.na(.), 0, .) %>% as.numeric(.) )) %>%
mutate(virus = ifelse( nVar %in% unique(vw_pos$nVar), "SARS-CoV-2", nVar))
f.fw_vw <- get_freq(data = fw_vw,
symptoms = s_list[["s.fw_vw_all"]] ,
virus) %>%
filter(symptom %in% s_list[["s.fw_vw_main"]]) %>%
mutate(virus = ifelse(virus == "seasonal coronavirus", "seasonal CoV", virus ),
symptom = factor(symptom,
levels = s_list[["s.fw_vw_main"]]))
# PLOT --------------------------------------------------------------------
.FW_VW_pal <- c(
"SARS-CoV-2" = "red",
"influenza" = "steelblue",
"RSV" = "forestgreen",
"rhinovirus" = "orange",
"seasonal CoV" = "#690fad")
.FW_VW_lty <- c(
"SARS-CoV-2" = "solid",
"influenza" = "solid",
"RSV" = "solid",
"rhinovirus" = "solid",
"seasonal CoV" = "solid")
yaxis <- tibble(y = seq(0,100, 20),
ylab = paste0(y, "%"))
p <- f.fw_vw %>%
ggplot(aes(x = symptom ,
y = frequency,
group =virus)) +
geom_ribbon(aes(
fill = virus,
ymin = lower_ci,
ymax = upper_ci),
alpha = 0.2,
show.legend = FALSE) +
geom_line(aes(
color = virus,
lty = virus )) +
geom_point(aes(
color = virus),
show.legend = FALSE) +
geom_hline(yintercept = seq(0,100, 20), colour = "gray", lty = "solid")+
geom_vline(xintercept = c(1:length(s_list[["s.fw_vw_main"]])),
colour = "gray", lty = "solid") +
geom_label(data = yaxis,
aes(x = 0.5,
y = y,
group = 1,
label = ylab),
fill = "white")+
annotate(geom = "line",
x = 1:4 ,
y = 100,
size = 1,
col = "steelblue")+
annotate(geom = "richtext",
x = median(1:4) ,
y = 100, label = "Respiratory",
col = "steelblue",
angle = -95 )+
annotate(geom = "line",
x = 4:7 ,
y = 100,
size = 1,
col = "#B97D4B")+
annotate(geom = "richtext",
x = median(4:7) ,
y = 100, label = "Constitutional",
col = "#B97D4B",
angle = 95 )+
scale_y_continuous(breaks = seq(0,100, 20))+
scale_color_manual(values = .FW_VW_pal)+
scale_fill_manual(values =.FW_VW_pal)+
scale_linetype_manual(values = .FW_VW_lty)+
theme_light()+
ggplot2::coord_polar(clip = "off")+
.polar_theme+
theme(legend.position = "bottom")+
labs(colour = "Virus", lty = "Virus")
p
ggsave(p,
width = width,
height = height,
unit = "cm",
file = paste0(save_path, "/figure 1.svg"))
# TABLE -------------------------------------------------------------------
f.fw_vw %>%
mutate(across(where(is.numeric), ~round(., digits = 1))) %>%
mutate(frequency = paste0(frequency,"(", lower_ci, "-", upper_ci, ")")) %>%
select(-c("lower_ci", "upper_ci")) %>%
select(-denominator) %>%
pivot_wider(names_from = virus, values_from = frequency) %>%
relocate(c("symptom", "SARS-CoV-2", "seasonal CoV")) %>%
flextable() %>%
flextable::save_as_docx(path = paste0(save_path, "/freqs_fw_vw.docx"))
width = 30
height = (9/16) * width
ggsave(p,
width = width,
height = height,
unit = "cm",
file = paste0(save_path, "/freqs_fw_vw.svg"))