Update 1-data-exploration.R
This commit is contained in:
parent
88be44b5e1
commit
ba22ffcce7
1 changed files with 26 additions and 10 deletions
|
@ -30,10 +30,10 @@ ds0 <- readr$read_rds(here("ML","data-unshared","ds_final.RDS"))
|
|||
|
||||
|
||||
ds1 <- ds0 %>%
|
||||
dplyr$select(-FT4, -subject_id, -charttime) %>%
|
||||
dplyr$select(-subject_id, -charttime) %>%
|
||||
dplyr$mutate(dplyr$across(
|
||||
ft4_dia
|
||||
, ~factor(., levels = c("Hypo", "Non-Hypo", "Normal TSH", "Hyper", "Non-Hyper")
|
||||
, ~factor(., levels = c("Hypo", "Non-Hypo","Hyper", "Non-Hyper")
|
||||
)
|
||||
)
|
||||
)
|
||||
|
@ -49,9 +49,8 @@ ds_recode <- ds1 %>%
|
|||
,~dplyr$recode(.
|
||||
,"Hypo" = 1
|
||||
,"Non-Hypo" = 2
|
||||
,"Normal TSH" = 3
|
||||
,"Hyper" = 4
|
||||
,"Non-Hyper" = 5
|
||||
,"Hyper" = 3
|
||||
,"Non-Hyper" = 4
|
||||
)
|
||||
)
|
||||
)
|
||||
|
@ -88,11 +87,18 @@ summary_tbl <- ds1 %>%
|
|||
|
||||
|
||||
# correlation plot
|
||||
ds_corr <- cor(ds_recode,use = "complete.obs")
|
||||
corr_plot <- cor(
|
||||
ds1 %>% dplyr$select(-gender,-ft4_dia)
|
||||
,use = "complete.obs"
|
||||
) %>%
|
||||
corrplot::corrplot(method = "number", type = "lower", tl.col = "black", tl.srt = 45
|
||||
,col = corrplot::COL1("Greys"))
|
||||
|
||||
# pick color blind friendly pallete
|
||||
|
||||
|
||||
#code for saving corr plot
|
||||
png(here("figures","corrplot.png"), type = 'cairo')
|
||||
devEMF::emf(here("figures","corrplot.emf"))
|
||||
corrplot::corrplot(ds_corr, method = "number")
|
||||
dev.off()
|
||||
|
||||
|
@ -112,8 +118,15 @@ g1 <- ds1 %>%
|
|||
|
||||
# g1
|
||||
|
||||
gp2$ggsave(
|
||||
here("figures","distrubution_histo.emf")
|
||||
,width = 7
|
||||
,height = 7
|
||||
,dpi = 300
|
||||
,device = devEMF::emf
|
||||
)
|
||||
|
||||
# this takes a bit to load. No discernable paterns in the data
|
||||
# this takes a bit to load. No discernible patterns in the data
|
||||
g2 <- ds_recode %>%
|
||||
dplyr$select(-gender) %>%
|
||||
dplyr$mutate(dplyr$across(-ft4_dia, log)) %>%
|
||||
|
@ -125,13 +138,16 @@ g2 <- ds_recode %>%
|
|||
gp2$theme_bw() +
|
||||
gp2$scale_fill_brewer(
|
||||
palette = "Greys"
|
||||
,labels = c("1 - Hypo","2 - Non-Hypo","3 - Normal TSH","4 - Hyper","5 - Non-Hyper")
|
||||
,labels = c("1 - Hypo","2 - Non-Hypo","3 - Hyper","4 - Non-Hyper")
|
||||
) +
|
||||
gp2$labs(
|
||||
x = NULL
|
||||
,y = NULL
|
||||
,fill = "Lab Diagnosis"
|
||||
,caption = "All values log transformed"
|
||||
,caption = "Note. All values log transformed"
|
||||
) +
|
||||
gp2$theme(
|
||||
plot.caption = gp2$element_text(hjust = 0)
|
||||
)
|
||||
|
||||
# g2
|
||||
|
|
Loading…
Reference in a new issue