From ba22ffcce7e8ce894c2c0732fc0969dacf1e3a52 Mon Sep 17 00:00:00 2001 From: Kyle Belanger Date: Tue, 24 Jan 2023 08:00:21 -0500 Subject: [PATCH] Update 1-data-exploration.R --- ML/1-data-exploration.R | 36 ++++++++++++++++++++++++++---------- 1 file changed, 26 insertions(+), 10 deletions(-) diff --git a/ML/1-data-exploration.R b/ML/1-data-exploration.R index 207feda..b5cdca2 100644 --- a/ML/1-data-exploration.R +++ b/ML/1-data-exploration.R @@ -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