plots: Change color palette

Change color palette to "lancet".

secmal.R

@@ -80,7 +80,7 @@ sma_plot_secmal_cmprsk <- function() {
 	cpr <- cuminc(secmal$time_at_risk / 365.25, secmal$time_at_risk_status)
 	ggcompetingrisks(cpr[1], conf.int = TRUE, multiple_panels = FALSE,
 			legend = "none", title = "", ylim = c(0:1),
-			xlab = "Years")
+			xlab = "Years", ggtheme = theme_bw(), palette = "lancet")
 }
 
 # Calculate cumuative risk with ci from cuminc.

survival.R

@@ -40,6 +40,7 @@ sma_plot_surv_asct <- function() {
 		   risk.table = "abs_pct",
 		   legend = "none",
 		   xlab = "Years",
+		   palette = "lancet",
 		   ggtheme = theme_bw())
 }
 
@@ -80,6 +81,7 @@ sma_plot_surv_sm <- function() {
 		   break.time.by = 365.25,
 		   legend = "none",
 		   xlab = "Years",
+		   palette = "lancet",
 		   ggtheme = theme_bw())
 }
 

utils.R

@@ -7,6 +7,7 @@ library(survival)
 library(survminer)
 library(tidyverse)
 library(cmprsk)
+library(ggsci)
 
 #
 # Write plot to filename

visualize.R

@@ -70,7 +70,10 @@ sma_jitt_dx_year <- function() {
 	ggplot(data, aes(x = asct_year, y = dx, colour = dx, fill = dx)) +
 		geom_jitter(width = 0.4, height = 0.2) +
 		labs(x = "Year", y = "Diagnosis") +
+		theme_bw() +
 		theme(legend.position = "none") +
+		scale_color_lancet() +
+		scale_fill_lancet() +
 		xlim(1990, 2020)
 }