Removing spliting of df and dfRef in get.ggplot

R/hypoAfrica.R

@@ -115,7 +115,6 @@ add.p.values.fisher<-function(df,dfRef,var,timeVar='visitid',nVar='total'){
 #' Plot comparison of measured and reference fractions
 #'
 #' @param df data frame of measured fractions
-#' @param dfRef data frame of reference fractions
 #' @param var target fraction variable
 #' @param timeVar variable measuring time
 #' @param doseVar variable for selecting datasets
@@ -123,8 +122,6 @@ add.p.values.fisher<-function(df,dfRef,var,timeVar='visitid',nVar='total'){
 #' @param doseBreaks values to break plots to
 #' @param doseLabels labels for legend for breaks
 #' @param doseColors colors to use for different plots
-#' @param timeBreaks where time points are assigned
-#' @param timeLabels labels for time points
 #'
 #' @return grob object with ggplot
 #'
@@ -132,18 +129,17 @@ add.p.values.fisher<-function(df,dfRef,var,timeVar='visitid',nVar='total'){
 #'
 #' @importFrom rlang .data
 #'
-get.ggplot<-function(df,dfRef,var,timeVar='visitid',doseVar='dose',nVar='total',
-   doseBreaks=base::c(60,62,100),doseLabels=base::c('60 Gy','62 Gy','all'),doseColors=base::c('red','magenta','blue'),
-   timeBreaks=base::c(0,1,3,4),timeLabels=base::c('beforeRT','at20','at3mo','at12mo')){
+get.ggplot<-function(df,var,timeVar='visitid',doseVar='dose',nVar='total',
+   doseBreaks=base::c(59.9,60,62,100),doseLabels=base::c('ref','60 Gy','62 Gy','all'),doseColors=base::c('grey70','red','magenta','blue')){
    df<-add.conf.int(df,var,nVar)
-   dfRef<-add.conf.int(dfRef,var,nVar)
+   #dfRef<-add.conf.int(dfRef,var,nVar)
 
    ghigh<-base::sprintf("%s_high",var)
    glow<-base::sprintf("%s_low",var)
    ggplot2::ggplot()+
-	ggplot2::geom_ribbon(ggplot2::aes(x=.data[[timeVar]],ymin=.data[[glow]],ymax=.data[[ghigh]]),dfRef,fill='grey70')+
+	#ggplot2::geom_ribbon(ggplot2::aes(x=.data[[timeVar]],ymin=.data[[glow]],ymax=.data[[ghigh]],dfRef,fill='grey70')+
 	ggplot2::geom_ribbon(ggplot2::aes(x=.data[[timeVar]],ymin=.data[[glow]],ymax=.data[[ghigh]],fill=base::as.factor(.data[[doseVar]])),df,alpha=0.2)+
-	ggplot2::geom_line(ggplot2::aes(x=.data[[timeVar]],y=.data[[var]]),dfRef)+
+	#ggplot2::geom_line(ggplot2::aes(x=.data[[timeVar]],y=.data[[var]]),dfRef)+
 	ggplot2::geom_line(ggplot2::aes(x=.data[[timeVar]],y=.data[[var]],color=base::as.factor(.data[[doseVar]])),df)+
 	ggplot2::scale_color_manual(name = "Dose", breaks = doseBreaks, values = doseColors,labels=doseLabels)+
 	ggplot2::scale_fill_manual(name = "Dose", breaks = doseBreaks, values = doseColors,labels=doseLabels)+