## ----include = FALSE---------------------------------------------------------- knitr::opts_chunk$set( collapse = TRUE, comment = "#>" ) ## ----setup, include = FALSE--------------------------------------------------- library(braidReports) set.seed(20240828) ## ----------------------------------------------------------------------------- concentrations <- c(0,2^(-3:3)) surface <- data.frame( concA = rep(rep(concentrations,each=length(concentrations)),each=3), concB = rep(rep(concentrations,times=length(concentrations)),each=3), replicate = rep(c(1,2,3),times=(length(concentrations)^2)) ) surface$actual <- evalBraidModel( surface$concA, surface$concB, c(1, 1, 3, 3, 2, 0, 100, 100, 100) ) surface$measure <- surface$actual + rnorm(nrow(surface),sd=7) head(surface, 12) ## ----warning=FALSE------------------------------------------------------------ ggplot(surface,aes(x=concA,y=measure,colour=factor(concB)))+ geom_point()+ stat_summary(geom="line",fun.data=mean_se)+ scale_x_log10()+ labs(x="Drug A",y="Effect",colour="Drug B") ## ----warning=FALSE------------------------------------------------------------ ggplot(surface, aes(x=concA,y=concB))+ stat_summary_2d(aes(z=measure), fun="mean")+ scale_x_log10()+ scale_y_log10()+ scale_fill_distiller(palette="RdYlBu")+ coord_equal()+ labs(x="Drug A",y="Drug B",fill="Effect") ## ----warning=FALSE------------------------------------------------------------ ggplot(surface,aes(x=concA,y=concB))+ geom_braid(aes(fill=measure))+ scale_x_log10()+ scale_y_log10()+ scale_fill_distiller(palette="RdYlBu")+ coord_equal()+ labs(x="Drug A",y="Drug B",fill="Effect") ## ----warning=FALSE------------------------------------------------------------ ggplot(surface,aes(x=concA,y=concB))+ geom_braid(aes(fill=measure))+ geom_point(colour="black")+ scale_x_log10("Drug A")+ scale_y_log10("Drug B")+ scale_fill_viridis_c("Effect",option="A")+ coord_equal()+ facet_wrap(vars(replicate)) ## ----warning=FALSE------------------------------------------------------------ surface$tilewidth <- log10(2)*0.9 surface$tilewidth[surface$concA==0] <- log10(2)/2 surface$tileheight <- log10(2)*0.9 surface$tileheight[surface$concB==0] <- log10(2)/2 ggplot(surface,aes(x=concA,y=concB))+ geom_braid(aes(fill=measure,width=tilewidth,height=tileheight),space=3)+ scale_x_log10("Drug A")+ scale_y_log10("Drug B")+ scale_fill_distiller("Effect",palette="RdYlBu")+ coord_equal() ## ----------------------------------------------------------------------------- glassSurface <- surface glassSurface$concA[glassSurface$replicate==2] <- glassSurface$concA[glassSurface$replicate==2]*1.25 glassSurface$concB[glassSurface$replicate==3] <- glassSurface$concB[glassSurface$replicate==3]*1.25 glassSurface$actual <- evalBraidModel( glassSurface$concA, glassSurface$concB, c(1, 1, 3, 3, -0.5, 0, 60, 100, 100) ) glassSurface$measure <- glassSurface$actual+rnorm(nrow(glassSurface),sd=7) head(glassSurface, 12) ## ----warning=FALSE------------------------------------------------------------ ggplot(glassSurface,aes(x=concA,y=concB))+ geom_braid(aes(fill=measure))+ geom_point(colour="black")+ scale_x_log10("Drug A")+ scale_y_log10("Drug B")+ scale_fill_distiller("Effect",palette="RdYlBu")+ coord_equal() ## ----warning=FALSE------------------------------------------------------------ ggplot(glassSurface,aes(x=concA,y=concB))+ geom_braid_glass(aes(fill=measure))+ geom_point(colour="black")+ scale_x_log10("Drug A")+ scale_y_log10("Drug B")+ scale_fill_distiller("Effect",palette="RdYlBu")+ coord_equal() ## ----warning=FALSE------------------------------------------------------------ ggplot(glassSurface,aes(x=concA,y=concB))+ geom_braid_glass(aes(fill=measure,width=tilewidth,height=tileheight),space=2)+ scale_x_log10("Drug A")+ scale_y_log10("Drug B")+ scale_fill_distiller("Effect",palette="RdYlBu")+ coord_equal() ## ----warning=FALSE------------------------------------------------------------ ggplot(surface,aes(x=concA,y=concB))+ geom_braid_smooth(aes(fill=measure))+ scale_x_log10()+ scale_y_log10()+ scale_fill_distiller(palette="RdYlBu")+ coord_equal()+ labs(x="Drug A",y="Drug B",fill="Effect") ## ----warning=FALSE------------------------------------------------------------ ggplot(glassSurface,aes(x=concA,y=concB))+ geom_braid_smooth(aes(fill=measure))+ geom_point(colour="black")+ scale_x_log10("Drug A")+ scale_y_log10("Drug B")+ scale_fill_distiller("Effect",palette="RdYlBu")+ coord_equal() ggplot(glassSurface,aes(x=concA,y=concB))+ geom_braid_smooth(aes(fill=measure,width=log10(2),height=log10(2)))+ scale_x_log10("Drug A")+ scale_y_log10("Drug B")+ scale_fill_distiller("Effect",palette="RdYlBu")+ coord_equal() ggplot(glassSurface,aes(x=concA,y=concB))+ geom_braid_smooth(aes(fill=measure,width=tilewidth,height=tileheight),space=2)+ scale_x_log10("Drug A")+ scale_y_log10("Drug B")+ scale_fill_distiller("Effect",palette="RdYlBu")+ coord_equal() ## ----warning=FALSE------------------------------------------------------------ ggplot(surface,aes(x=concA,y=concB))+ geom_braid_smooth(aes(fill=measure))+ geom_braid_contour(aes(z=measure),breaks=10*(1:9),colour="black",linetype=2)+ scale_x_log10()+ scale_y_log10()+ scale_fill_distiller(palette="RdYlBu")+ coord_equal()+ labs(x="Drug A",y="Drug B",fill="Effect") ## ----warning=FALSE------------------------------------------------------------ ggplot(glassSurface,aes(x=concA,y=concB))+ geom_braid_smooth(aes(fill=measure))+ geom_point(colour="black")+ geom_braid_contour(aes(z=measure),breaks=10*(1:9),colour="black",linetype=2)+ scale_x_log10("Drug A")+ scale_y_log10("Drug B")+ scale_fill_distiller("Effect",palette="RdYlBu")+ coord_equal() ggplot(glassSurface,aes(x=concA,y=concB))+ geom_braid_smooth(aes(fill=measure,width=tilewidth,height=tileheight),space=2)+ geom_braid_contour(aes(z=measure,width=tilewidth,height=tileheight),space=2, breaks=10*(1:9),colour="black",linetype=2)+ scale_x_log10("Drug A")+ scale_y_log10("Drug B")+ scale_fill_distiller("Effect",palette="RdYlBu")+ coord_equal() ## ----warning=FALSE------------------------------------------------------------ surface$type <- "Synergy" glassSurface$type <- "Antagonism" allSurface <- rbind(surface,glassSurface) allSurface$type <- factor(allSurface$type,c("Synergy","Antagonism")) ggplot(allSurface,aes(x=concA,y=concB,colour=type))+ geom_point()+ geom_braid_contour(aes(z=measure,width=tilewidth,height=tileheight), breaks=c(50,90), tight=TRUE)+ scale_x_log10()+ scale_y_log10()+ scale_color_brewer("Surface Type",palette="Set1")+ coord_equal()+ labs(x="Drug A",y="Drug B") ## ----------------------------------------------------------------------------- # With warnings enabled... ggplot(surface,aes(x=concA,y=concB))+ geom_braid(aes(fill=measure))+ scale_x_log10()+ scale_y_log10()+ scale_fill_distiller(palette="RdYlBu")+ coord_equal()+ labs(x="Drug A",y="Drug B",fill="Effect")