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Update 1-data-exploration.R

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Kyle Belanger 2023-01-22 15:26:39 -05:00
parent b2bffd959b
commit 2cc710650b
1 changed files with 16 additions and 6 deletions
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22
ML/1-data-exploration.R
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@ -116,25 +116,35 @@ g1 <- ds1 %>%
# this takes a bit to load. No discernable paterns in the data # this takes a bit to load. No discernable paterns in the data
g2 <- ds_recode %>% g2 <- ds_recode %>%
dplyr$select(-gender) %>% dplyr$select(-gender) %>%
dplyr$mutate(dplyr$across(-ft4_dia, log)) %>%
tidyr$pivot_longer(cols = !ft4_dia) %>% tidyr$pivot_longer(cols = !ft4_dia) %>%
ggplot(aes(x = factor(ft4_dia), y = value, fill = factor(ft4_dia))) + ggplot(aes(x = factor(ft4_dia), y = value, fill = factor(ft4_dia))) +
gp2$geom_boxplot(outlier.shape = NA, na.rm = TRUE) + gp2$stat_boxplot(geom = "errorbar", na.rm = TRUE) +
gp2$geom_jitter(size=.7, width=.1, alpha=.5, na.rm = TRUE) + gp2$geom_boxplot(na.rm = TRUE, outlier.shape = NA) +
gp2$facet_wrap(~name, scales = "free") + gp2$facet_wrap(~name, scales = "free") +
gp2$theme_bw() + gp2$theme_bw() +
gp2$scale_fill_brewer( gp2$scale_fill_brewer(
palette = "Greys" palette = "Greys"
,labels = c("Hypo","Non-Hypo","Normal TSH","Hyper","Non-Hyper") ,labels = c("1 - Hypo","2 - Non-Hypo","3 - Normal TSH","4 - Hyper","5 - Non-Hyper")
) + ) +
gp2$labs( gp2$labs(
x = NULL x = NULL
,y = NULL ,y = NULL
,fill = "Lab Diagnosis" ,fill = "Lab Diagnosis"
,caption = "All values log transformed"
) )
# g2 # g2
gp2$ggsave(
gp2$ggsave(here("figures","boxplot.png"), width = 7, height = 7, dpi = 300) here("figures","boxplot.emf")
,width = 7
,height = 7
,dpi = 300
,device = devEMF::emf
)