Skip to content

Commit

Permalink
Made plots more legible and proper size for PLOS ONE
Browse files Browse the repository at this point in the history
  • Loading branch information
@gaiusjaugustus
gaiusjaugustus committed Apr 13, 2018
1 parent 4d48b3b commit b8fc289
Show file tree
Hide file tree
Showing 6 changed files with 588 additions and 279 deletions.
574 changes: 464 additions & 110 deletions Code/.Rhistory
View file

Large diffs are not rendered by default.

15 changes: 9 additions & 6 deletions Code/DistantCRC_Figures_Fig2.Rmd
View file
Original file line number Diff line number Diff line change
Expand Up @@ -97,15 +97,18 @@ Figure2Export <- ggplot() +
theme_classic() +
theme(
legend.position = "bottom",
legend.title = element_text(size=12, face="bold"),
legend.text = element_text(size=10),
legend.title = element_text(size=7, face="bold"),
legend.text = element_text(size=6),
legend.title.align = 0.5,
axis.title = element_text(size = 12, face="bold"),
axis.text = element_text(size=10),
axis.text.x = element_text(angle=45, vjust=0.5)
legend.box.margin = margin(t=-10, b=-5),
axis.title = element_text(size = 7, face="bold"),
axis.text = element_text(size=6),
axis.text.x = element_text(angle=45, vjust=0.5),
plot.margin = unit(c(.5,.5,.25,.5), "lines")
)
Figure2Export
#ggsave(plot=Figure2Export, filename="Figure2.tiff", path="path/to/folder/DistantCRC_BriefComm", device = "tiff", width=16, height=10, units="cm", dpi = 300)
setwd("U:/Box Sync/Distant CRC - JNCI Brief Comm/DistantCRCRates/")
ggsave(plot=Figure2Export, filename="Figure2.tif", path="../", device = "tiff", width=3, height=2.5, units="in", dpi = 300)
```


Expand Down
34 changes: 20 additions & 14 deletions Code/DistantCRC_Figures_Fig2.nb.html
View file

Large diffs are not rendered by default.

88 changes: 37 additions & 51 deletions Code/DistantCRC_Figures_Fig3_cowplot.Rmd
View file
Original file line number Diff line number Diff line change
Expand Up @@ -61,9 +61,11 @@ Figure2A_themed <- Figure2A +
theme_classic() +
theme(
legend.position = "none",
axis.title = element_text(size = 12, face="bold"),
axis.text = element_text(size=10),
axis.text.x = element_text(angle=45, vjust=0.5)
axis.title = element_text(size = 14, face="bold"),
axis.text = element_text(size=12),
axis.text.x = element_text(angle=45, vjust=0.5),
strip.text = element_text(size=12),
plot.margin = unit(c(1,1,1,1), "lines")
)
Figure2A_themed
Expand Down Expand Up @@ -105,9 +107,11 @@ Figure2B_themed <- Figure2B +
theme_classic() +
theme(
legend.position = "none",
axis.title = element_text(size = 12, face="bold"),
axis.text = element_text(size=10),
axis.text.x = element_text(angle=45, vjust=0.5)
axis.title = element_text(size = 14, face="bold"),
axis.text = element_text(size=12),
axis.text.x = element_text(angle=45, vjust=0.5),
strip.text = element_text(size=12),
plot.margin = unit(c(1,1,1,1), "lines")
)
Figure2B_themed
Expand All @@ -116,48 +120,29 @@ Figure2B_themed
```

# C: Race
```{r, message=FALSE}
CRCSites <- readr::read_delim("K:/SEER_DataTables/SEER_2000-2014_CRC_StageDistribution_Race.txt", "\t", escape_double = FALSE, trim_ws = TRUE)
colnames(CRCSites) <- c("Year","Race", "Stage","Rate", "Count", "Population")

CRCSites2 <- CRCSites %>% filter(!grepl("-", Year)) %>% filter(Stage %in% c("Distant","Localized","Regional","Unknown/unstaged")) %>% filter(Year >= 1998) %>% filter(! Race %in% c("Unknown"))
CRCSites2$Year <- as.integer(CRCSites2$Year)
```



Group by Year, Race, Stage and Age, then summarize by each combination. Get total cases for each year/race/age group.
```{r}
CRCSites2$Stage <- factor(CRCSites2$Stage, levels=c("Unknown/unstaged","Localized","Regional","Distant"))
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
```{r}
CRCSites2
```

# Read in joinpoint models
## Read in joinpoint models
```{r}
library(readxl)
```

```{r}
AI_JPs <- read_excel("../Data/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)
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), APC=NULL)
A_JPs <- read_excel("../Data/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))
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))
B_JPs <- read_excel("../Data/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))
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))
W_JPs <- read_excel("../Data/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), X__1=NULL, X__2=NULL)
mutate(Race = "White") %>%
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), X__1=NULL, X__2=NULL)
AllRace_JPs <- rbind(AI_JPs, A_JPs, B_JPs, W_JPs)
```
Expand All @@ -169,7 +154,7 @@ AllRace_JPs <- rbind(AI_JPs, A_JPs, B_JPs, W_JPs)
```{r}
colorclasses <- c("Localized" = "#016b0b","Distant" = "#be0306","Regional" = "#ffb401")
shapes <- c(15, 17, 8)
shapes <- c(8, 15, 17)
lwds <- c(3, 2, 1)
```
Expand All @@ -189,7 +174,7 @@ Races_labeller <- function(variable,value){

```{r}
Figure2C <- ggplot() +
geom_point(data=CRCSites2 %>% filter(Stage != "Unknown/unstaged"), aes(x=Year, y=Rate, col=Stage, group=Stage, shape=Stage), size=2) +
geom_point(data=AllRace_JPs %>% filter(Stage != "Unknown/unstaged"), aes(x=Year, y=Rate, col=Stage, group=Stage, shape=Stage), size=2) +
geom_line(data=AllRace_JPs, aes(x=Year, y=Model, group=Stage, col=Stage)) +
facet_grid(. ~ Race, labeller = Races_labeller) +
scale_x_continuous(breaks=c(1998, 2000, 2005, 2010, 2014), labels = c("1998", "2000", "2005", "2010", "2014"), minor_breaks = seq(1998,2014,1)) +
Expand All @@ -203,9 +188,11 @@ Figure2C_themed <- Figure2C +
theme_classic() +
theme(
legend.position = "none",
axis.title = element_text(size = 12, face="bold"),
axis.text = element_text(size=10),
axis.text.x = element_text(angle=45, vjust=0.5)
axis.title = element_text(size = 14, face="bold"),
axis.text = element_text(size=12),
axis.text.x = element_text(angle=45, vjust=0.5),
strip.text = element_text(size=12),
plot.margin = unit(c(1,1,1,1), "lines")
)
Figure2C_themed
Expand Down Expand Up @@ -253,9 +240,11 @@ Figure2D_themed <- Figure2D +
theme_classic() +
theme(
legend.position = "none",
axis.title = element_text(size = 12, face="bold"),
axis.text = element_text(size=10),
axis.text.x = element_text(angle=45, vjust=0.5)
axis.title = element_text(size = 14, face="bold"),
axis.text = element_text(size=12),
axis.text.x = element_text(angle=45, vjust=0.5),
strip.text = element_text(size=12),
plot.margin = unit(c(1,1,1,1), "lines")
)
Figure2D_themed
Expand All @@ -264,23 +253,20 @@ Figure2D_themed
# Cowplot, put it all together
```{r}
Legend <- get_legend(Figure2B_themed + theme(legend.position = "bottom",
legend.title = element_text(size=12, face="bold"),
legend.text = element_text(size=10)))
legend.title = element_text(size=14, face="bold"),
legend.text = element_text(size=13)))
```



```{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)
prow <- plot_grid(Figure2A_themed, Figure2B_themed, Figure2C_themed, Figure2D_themed, labels = c("A", "B", "C", "D"), hjust = -1.25, 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)
setwd("U:/Box Sync/Distant CRC - JNCI Brief Comm/DistantCRCRates/")
ggsave(plot=p, filename="Figure3_1200px.tif", path="../", device = "tiff", width=13, height=9, 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)
```


Expand Down
Loading

0 comments on commit b8fc289

Please sign in to comment.