In modelistatistik/deneme: Template of R Codes Used in Histopathology Research

Plots

Categorical Variables

dependent <- c("Lauren",
               "CD44",
               "Her2",
               "MMR2",
                 "TumorPDL1gr1",
                 "TumorPDL1gr5",
                 "inflPDL1gr1",
                 "inflPDL1gr5"
                 )

explanatory <- c("Cinsiyet",
                 # "TumorYerlesimi",
                 "Lauren",
                 "Grade",
                 "T_stage",
                 "N_stage",
                 "M_stage",
                 "CD44",
                 "Her2",
                 "MMR2",
                 "TumorPDL1gr1",
                 "TumorPDL1gr5",
                 "inflPDL1gr1",
                 "inflPDL1gr5",
                 "LVI",
                 "PNI",
                 "LenfNoduMetastazi")

mydataCategorical <- mydata %>% 
    select(-Yas,
           -TumorCapi,
           -CerrahiTarih,
           -genel_sagkalim,
           -SonTarih,
           -TNM
    )

mydataCategorical_variable <- explanatory[1]
dependent2 <- dependent[!dependent %in% mydataCategorical_variable]
source(here::here("R", "generatingCodeForCategoricalPlots.R"))

mydataCategorical_variable <- NA
dependent2 <- NA
mydataCategorical_variable <- explanatory[2]
dependent2 <- dependent[!dependent %in% mydataCategorical_variable]
source(here::here("R", "generatingCodeForCategoricalPlots.R"))

mydataCategorical_variable <- NA
dependent2 <- NA
mydataCategorical_variable <- explanatory[3]
dependent2 <- dependent[!dependent %in% mydataCategorical_variable]
source(here::here("R", "generatingCodeForCategoricalPlots.R"))

mydataCategorical_variable <- NA
dependent2 <- NA
mydataCategorical_variable <- explanatory[4]
dependent2 <- dependent[!dependent %in% mydataCategorical_variable]
source(here::here("R", "generatingCodeForCategoricalPlots.R"))

mydataCategorical_variable <- NA
dependent2 <- NA
mydataCategorical_variable <- explanatory[5]
dependent2 <- dependent[!dependent %in% mydataCategorical_variable]
source(here::here("R", "generatingCodeForCategoricalPlots.R"))

mydataCategorical_variable <- NA
dependent2 <- NA
mydataCategorical_variable <- explanatory[6]
dependent2 <- dependent[!dependent %in% mydataCategorical_variable]
source(here::here("R", "generatingCodeForCategoricalPlots.R"))

mydataCategorical_variable <- NA
dependent2 <- NA
mydataCategorical_variable <- explanatory[7]
dependent2 <- dependent[!dependent %in% mydataCategorical_variable]
source(here::here("R", "generatingCodeForCategoricalPlots.R"))

mydataCategorical_variable <- NA
dependent2 <- NA
mydataCategorical_variable <- explanatory[8]
dependent2 <- dependent[!dependent %in% mydataCategorical_variable]
source(here::here("R", "generatingCodeForCategoricalPlots.R"))

mydataCategorical_variable <- NA
dependent2 <- NA
mydataCategorical_variable <- explanatory[9]
dependent2 <- dependent[!dependent %in% mydataCategorical_variable]
source(here::here("R", "generatingCodeForCategoricalPlots.R"))

mydataCategorical_variable <- NA
dependent2 <- NA
mydataCategorical_variable <- explanatory[10]
dependent2 <- dependent[!dependent %in% mydataCategorical_variable]
source(here::here("R", "generatingCodeForCategoricalPlots.R"))

mydataCategorical_variable <- NA
dependent2 <- NA
mydataCategorical_variable <- explanatory[11]
dependent2 <- dependent[!dependent %in% mydataCategorical_variable]
source(here::here("R", "generatingCodeForCategoricalPlots.R"))

mydataCategorical_variable <- NA
dependent2 <- NA
mydataCategorical_variable <- explanatory[12]
dependent2 <- dependent[!dependent %in% mydataCategorical_variable]
source(here::here("R", "generatingCodeForCategoricalPlots.R"))

mydataCategorical_variable <- NA
dependent2 <- NA
mydataCategorical_variable <- explanatory[13]
dependent2 <- dependent[!dependent %in% mydataCategorical_variable]
source(here::here("R", "generatingCodeForCategoricalPlots.R"))

mydataCategorical_variable <- NA
dependent2 <- NA
mydataCategorical_variable <- explanatory[14]
dependent2 <- dependent[!dependent %in% mydataCategorical_variable]
source(here::here("R", "generatingCodeForCategoricalPlots.R"))

mydataCategorical_variable <- NA
dependent2 <- NA
mydataCategorical_variable <- explanatory[15]
dependent2 <- dependent[!dependent %in% mydataCategorical_variable]
source(here::here("R", "generatingCodeForCategoricalPlots.R"))

mydataCategorical_variable <- NA
dependent2 <- NA
mydataCategorical_variable <- explanatory[16]
dependent2 <- dependent[!dependent %in% mydataCategorical_variable]
source(here::here("R", "generatingCodeForCategoricalPlots.R"))

Plots

Continious Variables

# mydataContinious

mydata %>%
    select(institution, starts_with("Slide")) %>%
    pivot_longer(cols = starts_with("Slide")) %>%
    ggplot(., aes(name, value)) -> p
p + geom_jitter() 
p + geom_jitter(aes(colour = institution))

dxchanges <- mydata %>%
    select(bx_no, starts_with("Slide")) %>% 
    filter(complete.cases(.)) %>%
    group_by(Slide1_infiltrative, Slide2_Medium, Slide3_Demarcated) %>% 
    tally()

library(ggalluvial)

ggplot(data = dxchanges,
       aes(axis1 = Slide1_infiltrative, axis2 = Slide2_Medium, axis3 = Slide3_Demarcated,
           y = n)) +
  scale_x_discrete(limits = c("Slide1", "Slide2", "Slide3"),
                   expand = c(.1, .05)
                   ) +
  xlab("Slide") +
  geom_alluvium(aes(fill = Slide1_infiltrative,
                    colour = Slide1_infiltrative
                    )) +
  geom_stratum() +
  geom_text(stat = "stratum", label.strata = TRUE) +
  theme_minimal() +
  ggtitle("PanNET")