Updated code for new submission to BMC Cancer

Code/DistantCRC_Figures_Fig3_cowplot.Rmd

@@ -16,31 +16,25 @@ library(readxl)
 library(cowplot)
 ```
 
-```{r, echo=FALSE}
-directory <- "U:/Box Sync/ProjectDocs/2017_DistantCRC/JoinPoint/"
-```
-
-
 
 # A: Age
 ```{r}
 library(readxl)
 ```
 
-Read in joinpoint model excel sheeets
+
 ```{r}
-Early_JP <- read_excel(paste0(directory, "Rate_StageEarly.xlsx")) %>% rename("Year" = "X Value", "Model" = "Modeleded Y Value", "Rate" = "Observed Y Value") %>% mutate(Year = as.integer(Year), Model = as.numeric(Model), Rate = as.numeric(Rate), AgeCategory = "Early")
-Middle_JP <- read_excel(paste0(directory, "Rate_StageMiddle.xlsx")) %>% rename("Year" = "X Value", "Model" = "Modeleded Y Value", "Rate" = "Observed Y Value") %>% mutate(Year = as.integer(Year), Model = as.numeric(Model), Rate = as.numeric(Rate), AgeCategory = "Middle")
-Late_JP <- read_excel(paste0(directory, "Rate_StageLate.xlsx")) %>% rename("Year" = "X Value", "Model" = "Modeleded Y Value", "Rate" = "Observed Y Value") %>% mutate(Year = as.integer(Year), Model = as.numeric(Model), Rate = as.numeric(Rate), AgeCategory = "Late")
+Early_JP <- read_excel("U:/Box Sync/ProjectDocs/2017_DistantCRC/JoinPoint/Rate_StageEarly.xlsx") %>% rename("Year" = "X Value", "Model" = "Modeleded Y Value", "Rate" = "Observed Y Value") %>% mutate(Year = as.integer(Year), Model = as.numeric(Model), Rate = as.numeric(Rate), AgeCategory = "Early")
+Middle_JP <- read_excel("U:/Box Sync/ProjectDocs/2017_DistantCRC/JoinPoint/Rate_StageMiddle.xlsx") %>% rename("Year" = "X Value", "Model" = "Modeleded Y Value", "Rate" = "Observed Y Value") %>% mutate(Year = as.integer(Year), Model = as.numeric(Model), Rate = as.numeric(Rate), AgeCategory = "Middle")
+Late_JP <- read_excel("U:/Box Sync/ProjectDocs/2017_DistantCRC/JoinPoint/Rate_StageLate.xlsx") %>% rename("Year" = "X Value", "Model" = "Modeleded Y Value", "Rate" = "Observed Y Value") %>% mutate(Year = as.integer(Year), Model = as.numeric(Model), Rate = as.numeric(Rate), AgeCategory = "Late")
 
 AllAges_JP <- rbind(Early_JP, Middle_JP, Late_JP)
 AllAges_JP$AgeCategory <- factor(AllAges_JP$AgeCategory, levels = c("Early","Middle","Late"))
 ```
 
 
-## Plots
+# Plots
 
-Set aesthetic scale options
 ```{r}
 colorclasses <- c("Localized" = "#016b0b","Distant" = "#be0306","Regional" = "#ffb401")
 
@@ -76,20 +70,18 @@ Figure2A_themed
 ```
 
 # B: Sidedness
-
-Read in joinpoint model outputs
 ```{r}
-Prox_JP <- read_excel(paste0(directory, "Rate_StageProximal.xlsx")) %>% rename("Year" = "X Value", "Rate" = "Observed Y Value", "Model" = "Modeleded Y Value") %>% mutate(Year = as.integer(Year), Rate = as.numeric(Rate), Model = as.numeric(Model), Side = "Proximal")
-Dist_JP <- read_excel(paste0(directory, "Rate_StageDistal.xlsx")) %>% rename("Year" = "X Value", "Rate" = "Observed Y Value", "Model" = "Modeleded Y Value") %>% mutate(Year = as.integer(Year), Rate = as.numeric(Rate), Model = as.numeric(Model), Side = "Distal")
+Prox_JP <- read_excel("U:/Box Sync/ProjectDocs/2017_DistantCRC/JoinPoint/Rate_StageProximal.xlsx") %>% rename("Year" = "X Value", "Rate" = "Observed Y Value", "Model" = "Modeleded Y Value") %>% mutate(Year = as.integer(Year), Rate = as.numeric(Rate), Model = as.numeric(Model), Side = "Proximal")
+Dist_JP <- read_excel("U:/Box Sync/ProjectDocs/2017_DistantCRC/JoinPoint/Rate_StageDistal.xlsx") %>% rename("Year" = "X Value", "Rate" = "Observed Y Value", "Model" = "Modeleded Y Value") %>% mutate(Year = as.integer(Year), Rate = as.numeric(Rate), Model = as.numeric(Model), Side = "Distal")
 
 AllSides_JP <- rbind(Prox_JP, Dist_JP)
 AllSides_JP$Side <- factor(AllSides_JP$Side, levels=c("Proximal","Distal"))
 AllSides_JP$Stage <- factor(AllSides_JP$Stage, levels = c("Localized","Regional","Distant"))
 ```
 
 
-## Plots   
-Set aesthetic scale options
+#Plots
+
 ```{r}
 colorclasses <- c("Localized" = "#016b0b", "Distant" = "#be0306", "Regional" = "#ffb401")
 
@@ -98,7 +90,7 @@ lwds <- c(3, 4, 2, 1)
 ```
 
 
-## Rate of Disease Stage by Site Category over time
+##Rate of Disease Stage by Site Category over time
 ```{r}
 Figure2B <- ggplot(AllSides_JP) + 
      geom_point(aes(x=Year, y=Rate, col=Stage, group=Stage, shape=Stage), size=2) + 
@@ -140,29 +132,29 @@ CRCSites2$Stage <- factor(CRCSites2$Stage, levels=c("Unknown/unstaged","Localize
 CRCSites2$Race <- factor(CRCSites2$Race, levels=c("Black", "American Indian/Alaska Native","Asian or Pacific Islander","White"), labels = c("Black or African American", "American Indian/Alaska Native","Asian or Pacific Islander","White"))
 ```
 
-## The Data we're working with
+# The Data we're working with
 ```{r}
 CRCSites2
 ```
 
-## Read in joinpoint models
+# Read in joinpoint models
 ```{r}
 library(readxl)
 ```
 
 ```{r}
-AI_JPs <- read_excel(paste0(directory, "Rate_StageAmericanIndian.xlsx"), sheet=3) %>% mutate(Race = "American Indian/Alaska Native") %>% rename("Year" = "X Value", "Model" = "Modeleded Y Value") %>% mutate(Year = as.integer(Year), Model = as.numeric(Model), APC=NULL)
-A_JPs <- read_excel(paste0(directory, "Rate_StageAsian.xlsx"), sheet=3) %>% mutate(Race = "Asian or Pacific Islander") %>% rename("Year" = "X Value", "Model" = "Modeleded Y Value") %>% mutate(Year = as.integer(Year), Model = as.numeric(Model))
-B_JPs <- read_excel(paste0(directory, "Rate_StageBlack.xlsx"), sheet=1) %>% mutate(Race = "Black or African American") %>% rename("Year" = "X Value", "Model" = "Modeleded Y Value") %>% mutate(Year = as.integer(Year), Model = as.numeric(Model))
-W_JPs <- read_excel(paste0(directory, "Rate_StageWhite.xlsx"), sheet=1) %>% mutate(Race = "White") %>% rename("Year" = "X Value", "Model" = "Modeleded Y Value") %>% mutate(Year = as.integer(Year), Model = as.numeric(Model))
+AI_JPs <- read_excel("U:/Box Sync/ProjectDocs/2017_DistantCRC/JoinPoint/Rate_StageAmericanIndian.xlsx", sheet=3) %>% mutate(Race = "American Indian/Alaska Native") %>% rename("Year" = "X Value", "Model" = "Modeleded Y Value") %>% mutate(Year = as.integer(Year), Model = as.numeric(Model), APC=NULL)
+A_JPs <- read_excel("U:/Box Sync/ProjectDocs/2017_DistantCRC/JoinPoint/Rate_StageAsian.xlsx", sheet=3) %>% mutate(Race = "Asian or Pacific Islander") %>% rename("Year" = "X Value", "Model" = "Modeleded Y Value") %>% mutate(Year = as.integer(Year), Model = as.numeric(Model))
+B_JPs <- read_excel("U:/Box Sync/ProjectDocs/2017_DistantCRC/JoinPoint/Rate_StageBlack.xlsx", sheet=1) %>% mutate(Race = "Black or African American") %>% rename("Year" = "X Value", "Model" = "Modeleded Y Value") %>% mutate(Year = as.integer(Year), Model = as.numeric(Model))
+W_JPs <- read_excel("U:/Box Sync/ProjectDocs/2017_DistantCRC/JoinPoint/Rate_StageWhite.xlsx", sheet=1) %>% mutate(Race = "White") %>% rename("Year" = "X Value", "Model" = "Modeleded Y Value") %>% mutate(Year = as.integer(Year), Model = as.numeric(Model))
 
 AllRace_JPs <- rbind(AI_JPs, A_JPs, B_JPs, W_JPs)
 ```
 
 
 
-##Rate of stage category by year    
-Set aesthetic scale options
+##Rate of stage category by year
+
 ```{r}
 colorclasses <- c("Localized" = "#016b0b","Distant" = "#be0306","Regional" = "#ffb401")
 
@@ -206,21 +198,22 @@ Figure2C_themed <- Figure2C +
      )
 
 Figure2C_themed
+
+#ggsave(plot=Figure2C_themed, filename="Figure2C.tiff", path="C:/Users/gaugustus/Documents/Success_Docs/Pubs/DistantCRC_BriefComm/", device = "tiff", width=16, height=10, units="cm", dpi = 300)
+
 ```
 
 # D: Sex
-
-Read in joinpoint model data
 ```{r}
-RateFemale_JP <- read_excel(paste0(directory, "Rate_StageFemale.xlsx")) %>% rename("Year" = "X Value", "Rate" = "Observed Y Value", "Model" = "Modeleded Y Value") %>% mutate(Year = as.integer(Year), Rate = as.numeric(Rate), Model = as.numeric(Model), Sex = "Female")
-RateMale_JP <- read_excel(paste0(directory, "Rate_StageFemale.xlsx")) %>% rename("Year" = "X Value", "Rate" = "Observed Y Value", "Model" = "Modeleded Y Value") %>% mutate(Year = as.integer(Year), Rate = as.numeric(Rate), Model = as.numeric(Model), Sex = "Male")
+RateFemale_JP <- read_excel("U:/Box Sync/ProjectDocs/2017_DistantCRC/JoinPoint/Rate_StageFemale.xlsx") %>% rename("Year" = "X Value", "Rate" = "Observed Y Value", "Model" = "Modeleded Y Value") %>% mutate(Year = as.integer(Year), Rate = as.numeric(Rate), Model = as.numeric(Model), Sex = "Female")
+RateMale_JP <- read_excel("U:/Box Sync/ProjectDocs/2017_DistantCRC/JoinPoint/Rate_StageFemale.xlsx") %>% rename("Year" = "X Value", "Rate" = "Observed Y Value", "Model" = "Modeleded Y Value") %>% mutate(Year = as.integer(Year), Rate = as.numeric(Rate), Model = as.numeric(Model), Sex = "Male")
 
 AllSex_JP <- rbind(RateFemale_JP, RateMale_JP)
 
 ```
 
 
-## Plots
+#Plots
 
 ```{r}
 colorclasses <- c("Localized" = "#016b0b", "Distant" = "#be0306", "Regional" = "#ffb401")
@@ -230,7 +223,7 @@ lwds <- c(3, 4, 2, 1)
 ```
 
 
-## Rate of Disease Stage by Site Category over time
+##Rate of Disease Stage by Site Category over time
 ```{r}
 Figure2D <- ggplot(AllSex_JP) + 
      geom_point(aes(x=Year, y=Rate, col=Stage, group=Stage, shape=Stage), size=2) + 
@@ -261,11 +254,18 @@ Legend <- get_legend(Figure2B_themed + theme(legend.position = "bottom",
 ```
 
 
+
 ```{r}
 prow <- plot_grid(Figure2A_themed, Figure2B_themed, Figure2C_themed, Figure2D_themed, labels = c("A", "B", "C", "D"), hjust = -1, nrow = 2, align = "vh", label_size = 26)
 p <- plot_grid(prow, Legend, ncol=1, rel_heights = c(1, .1))
 p
+#ggsave(plot=p, filename="Figure2.tiff", path="C:/Users/gaugustus/Documents/Success_Docs/Pubs/DistantCRC_BriefComm", device = "tiff", width=33, height=20, units="cm", dpi = 300)
+
+#ggsave(plot=p, filename="Figure2_Proof.tiff", path="C:/Users/gaugustus/Documents/Success_Docs/Pubs/DistantCRC_BriefComm", device = "tiff", width=33, height=20, units="cm", dpi = 72)
+
+ggsave(plot=p, filename="Figure3_1200px.tiff", path="U:/Box Sync/Distant CRC - JNCI Brief Comm", device = "tiff", width=12, height=7.5, units = "in", dpi=100)
 
+ggsave(plot=p, filename="Figure3.tiff", path="U:/Box Sync/Distant CRC - JNCI Brief Comm", device = "tiff", width=12, height=7.5, units = "in", dpi=300)
 ```