nov

snail_mesocosm.Rmd

@@ -196,46 +196,22 @@ cex_diam <- meso1$Diameter/3
 
 ### Set plotting graphics  
 ```{r, cache = TRUE, tidy = TRUE, lazy = TRUE, results="hide"}
-plot_it <- function(manuscript,bg,cp,alpha,family){ # plotting function (plot for MS or not, set bg color, set color palette from RColorBrewer, set alpha value for transperancy) 
-  graphics.off()
-  if(manuscript==0){
-    if(bg=="black"){
-      colvec<-magma(200,1)
-      par(bg = colvec[1],col.axis="white",col.lab="white",col.main="white",fg="white",bty="n",las=1,mar=c(5,6,4,2),family=family) #mono
-      border=adjustcolor("purple",alpha=0.5)
-    }else{
-      colvec<-bpy.colors(200)
-      par(bg = colvec[1],col.axis="white",col.lab="white",col.main="white",fg="white",bty="n",las=1,mar=c(5,6,4,2),family=family) 
-      border=adjustcolor("blue",alpha=0.5)
-    }
-  }else{
-#    graphics.off()
-    par(bty="n",las=1,family=family) 
-  }
-  # color palettes
-  # ifelse(manuscript==1,colvec<-adjustcolor(brewer.pal(9,cp)[9], alpha = alpha),colvec <- adjustcolor(brewer.pal(9,cp)[5], alpha = alpha)) # fine tune plotting colors for plotting bg
-   # colfunc <<- colorRampPalette(brewer.pal(9,cp),alpha=alpha)
-  colfunc <<- adjustcolor(brewer.pal(9,cp),alpha=alpha) # USES <<- OPERATOR
-}
+require(RCurl)
+script <- getURL("https://raw.githubusercontent.com/darwinanddavis/plot_it/master/plot_it.R", ssl.verifypeer = FALSE)
+eval(parse(text = script))
 
-# Setting ggplot theme graphics
-plot_it_gg <- function(bg){ # bg = colour to plot bg, family = font family
-  if(bg=="white"){
-    bg <- "white"
-    fg <- "black"
-  theme_tufte(base_family = "HersheySans") +
-    theme(panel.border = element_blank(),panel.grid.major = element_blank(),panel.grid.minor = element_blank(),panel.background = element_rect(fill = bg,colour = bg),plot.background = element_rect(fill=bg)) +
-    theme(axis.line = element_line(color = fg)) +theme(axis.ticks = element_line(color = fg)) + theme(plot.title = element_text(colour = fg)) +theme(axis.title.x = element_text(colour = fg), axis.title.y = element_text(colour = fg)) + theme(axis.text.x = element_text(color = fg),axis.text.y = element_text(color = fg)) + theme(legend.key = element_rect(fill = bg)) + theme(legend.title = element_text(colour=fg)) + theme(legend.text = element_text(colour=fg))
-}
-  }# end gg
 ```
 
 Set plotting parameters  
 
 ```{r, cache = TRUE, tidy = TRUE, lazy=TRUE, results="hide"}
-print("1/0, set colour, set colour palette 'display.brewer.all()',set alpha for col,set font")
-plot_it(0,"blue","YlOrRd",1,"HersheySans") # set col function params
-plot_it_gg("white") # same as above
+require(RColorBrewer)
+display.brewer.all()
+# Set global plotting parameters
+cat("plot_it( \n0 for presentation, 1 for manuscript, \nset colour for background, \nset colour palette 1. use 'display.brewer.all()', \nset colour palette 2. use 'display.brewer.all()', \nset alpha for colour transperancy, \nset font style \n)")
+
+plot_it(0,"blue","Spectral","Greens",1,"mono") # set plot function params     
+plot_it_gg("white") # same as above for ggplot    
 
 # set colors you want
 col <- "lightblue"