R基本绘图功能：图形的图例不正确

Question

I am having difficulties with the plot legends:

    head(bee.ground)
  X Month Treatment Block Bee_Richness Bee_Abundance  Bare Grass  Forb  Dead Moss
1 1   May        DS     1            0             0 23.20 15.72 37.80 17.00    0
2 2   May        GS     1            0             0 33.52 21.88 33.60  9.88    0
3 3   May        UB     1            1             1  0.60 18.28 35.00 43.48    0
4 4   May        DS     2            7            71 11.20 11.20 58.80 16.68    0
5 5   May        GS     2            5             6 37.00 12.08 43.92  5.12    0
6 6   May        UB     2            5            16  4.40 14.88 12.32 67.88    0

    shape<-as.numeric(as.factor(bee.ground$Block))
    color<-as.numeric(as.factor(bee.ground$Treatment))

    plot(bee.ground$Bare, bee.ground$Bee_Richness, main = "Bee Richness and Bare Ground Cover", 
 xlab = "Percent Bare Ground", ylab = "Bee Richness",
 pch = shape,
 col = color,
 las = 1,
 cex = 1.5)

test graph

This is the nice graph I get, which I think the black is DS, red is GS, and green is UB for treatments. The blocks (four different shapes) seem to be correct as well. However, when I make a legend with these same parameters, I get this: legend's in the top corner...

legend("topleft", 
   pch = shape, 
   col = color, 
   legend = c("Block 1","Block 2","Block 3","Block 4", NA, "DS","GS","UB"))

All it is doing is repeating the shape three times with alternating colors, instead of matching with what (I think) the graph is showing. I tried the merge function, but that did not correct the issue (it produces the same incorrect legend).

~Is there also a way in the plot function to make the legend go underneath the graph and centered? EDIT: I figured this out! just adjusted the ylim to go -3 and left space for a horizontal legend.

~Maybe another thing; how do I specifically assign each Treatment a specific color and each Block a specific shape, instead of letting R just use the first few options?

Thank you for your help!

EDIT: I ended up making two separate legends to destinguish between the blocks and treatments.

shape <- ifelse(bee.ground$Block == "1", 1,ifelse(bee.ground$Block == "2", 2, ifelse(bee.ground$Block == "3",3,4)))
color <- ifelse(bee.ground$Treatment == "DS", 'red',ifelse(bee.ground$Treatment == "GS", 'green', 'black'))

plot(bee.ground$Bare, bee.ground$Bee_Richness, main = "Bee Richness and Bare Ground Cover", 
     xlab = "Percent Bare Ground", ylab = "Bee Richness",pch = c(shape),
     col = c(color),las = 1,cex = 1.5,ylim = c(0,35))
legend("topleft", c('1','2','3','4'),pch = c(1,2,3,4),horiz = TRUE,title = "Block")
legend("topright",c("DS","GS","UB"),horiz = TRUE, text.col = c("red","green","black"),title = "Treatment",title.col = "black")

Answer 1

Perhaps this might help. I specified the shapes and colors I wanted for the plot and for the legend .

shape <- as.numeric(as.factor(bee.ground$Block))
color <- as.numeric(as.factor(bee.ground$Treatment))

plot(bee.ground$Bare, bee.ground$Bee_Richness, 
     main = "Bee Richness and Bare Ground Cover", 
     xlab = "Percent Bare Ground", ylab = "Bee Richness",
     pch = shape, col = color, las = 1, cex = 1.5)

     legend("topleft", c('Block DS, Treatment 1',
                         'Block DS, Treatment 2',
                         'Block DS, Treatment 3',
                         'Block GS, Treatment 1',
                         'Block GS, Treatment 2',
                         'Block GS, Treatment 3',
                         'Block UB, Treatment 1',
                         'Block UB, Treatment 2',
                         'Block UB, Treatment 3'),
                       pch = c(1,1,1,2,2,2,3,3,3), 
                       col = c('blue', 'green', 'brown', 
                               'blue', 'green', 'brown',
                               'blue', 'green', 'brown'))


shape <- ifelse(bee.ground$Block == 'DS', 3,
         ifelse(bee.ground$Block == 'GS', 6, 9))

color <- ifelse(bee.ground$Treatment == 1, 'red',
         ifelse(bee.ground$Treatment == 2, 'blue', 'black'))

plot(bee.ground$Bare, bee.ground$Bee_Richness, 
     main = "Bee Richness and Bare Ground Cover", 
     xlab = "Percent Bare Ground", ylab = "Bee Richness",
     pch = shape, col = color, las = 1, cex = 1.5)

     legend("topleft", c('Block DS, Treatment 1',
                         'Block DS, Treatment 2',
                         'Block DS, Treatment 3',
                         'Block GS, Treatment 1',
                         'Block GS, Treatment 2',
                         'Block GS, Treatment 3',
                         'Block UB, Treatment 1',
                         'Block UB, Treatment 2',
                         'Block UB, Treatment 3'),
                       pch = c(3,3,3,6,6,6,9,9,9), 
                       col = c('red', 'blue', 'black',
                               'red', 'blue', 'black',
                               'red', 'blue', 'black'))