I am handling this data:
dput(data.mi10)
structure(list(Days = c(0, 40.5555555555556, 81.1111111111111,
121.666666666667, 162.222222222222, 202.777777777778, 243.333333333333,
283.888888888889, 324.444444444444, 365, 0, 40.5555555555556,
81.1111111111111, 121.666666666667, 162.222222222222, 202.777777777778,
243.333333333333, 283.888888888889, 324.444444444444, 365, 0,
40.5555555555556, 81.1111111111111, 121.666666666667, 162.222222222222,
202.777777777778, 243.333333333333, 283.888888888889, 324.444444444444,
365, 0, 40.5555555555556, 81.1111111111111, 121.666666666667,
162.222222222222, 202.777777777778, 243.333333333333, 283.888888888889,
324.444444444444, 365, 0, 40.5555555555556, 81.1111111111111,
121.666666666667, 162.222222222222, 202.777777777778, 243.333333333333,
283.888888888889, 324.444444444444, 365, 0, 40.5555555555556,
81.1111111111111, 121.666666666667, 162.222222222222, 202.777777777778,
243.333333333333, 283.888888888889, 324.444444444444, 365, 0,
40.5555555555556, 81.1111111111111, 121.666666666667, 162.222222222222,
202.777777777778, 243.333333333333, 283.888888888889, 324.444444444444,
365, 0, 40.5555555555556, 81.1111111111111, 121.666666666667,
162.222222222222, 202.777777777778, 243.333333333333, 283.888888888889,
324.444444444444, 365), Shannon = c(3.60331931049121, 3.60331931049121,
3.60331931049121, 3.60331931049121, 3.60331931049121, 3.60331931049121,
3.60331931049121, 3.60331931049121, 3.60331931049121, 3.60331931049121,
3.66591200730046, 3.66591200730046, 3.66591200730046, 3.66591200730046,
3.66591200730046, 3.66591200730046, 3.66591200730046, 3.66591200730046,
3.66591200730046, 3.66591200730046, 3.72850470410971, 3.72850470410971,
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117.302821326582, 115.558301120658, 114.40557579644, 113.726286377587,
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73.4669715525888, 71.2699929987449, 70.1836258115174, 69.8564321663107,
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40.5555555555556, 81.1111111111111, 121.666666666667, 162.222222222222,
202.777777777778, 243.333333333333, 283.888888888889, 324.444444444444,
365, 0, 40.5555555555556, 81.1111111111111, 121.666666666667,
162.222222222222, 202.777777777778, 243.333333333333, 283.888888888889,
324.444444444444, 365, 0, 40.5555555555556, 81.1111111111111,
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283.888888888889, 324.444444444444, 365, 0, 40.5555555555556,
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40.5555555555556, 81.1111111111111, 121.666666666667, 162.222222222222,
202.777777777778, 243.333333333333, 283.888888888889, 324.444444444444,
365, 0, 40.5555555555556, 81.1111111111111, 121.666666666667,
162.222222222222, 202.777777777778, 243.333333333333, 283.888888888889,
324.444444444444, 365, 0, 40.5555555555556, 81.1111111111111,
121.666666666667, 162.222222222222, 202.777777777778, 243.333333333333,
283.888888888889, 324.444444444444, 365, 0, 40.5555555555556,
81.1111111111111, 121.666666666667, 162.222222222222, 202.777777777778,
243.333333333333, 283.888888888889, 324.444444444444, 365), xvar = c(3.60331931049121,
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4.04146818815597, 4.04146818815597, 4.04146818815597, 4.04146818815597,
4.04146818815597, 4.04146818815597, 4.04146818815597)), class = "data.frame", row.names = c("1",
"2", "3", "4", "5", "6", "7", "8", "9", "10", "11", "12", "13",
"14", "15", "16", "17", "18", "19", "20", "21", "22", "23", "24",
"25", "26", "27", "28", "29", "30", "31", "32", "33", "34", "35",
"36", "37", "38", "39", "40", "41", "42", "43", "44", "45", "46",
"47", "48", "49", "50", "51", "52", "53", "54", "55", "56", "57",
"58", "59", "60", "61", "62", "63", "64", "65", "66", "67", "68",
"69", "70", "71", "72", "73", "74", "75", "76", "77", "78", "79",
"80"))
where I am trying to plot some data using this script:
scale.breaks = scales::fullseq(range(data.mi10$yvar), size = 0.01)
ggplot(data= data.mi10 , aes(x= Days, y= Shannon, z= yvar))
geom_contour_filled(breaks = scale.breaks)
geom_contour(data= data.mi10,aes(x = Days, y = Shannon, z = yvar), color= 'black', bins= 15, alpha=0.25)
xlab('Time (days)')
ylab('Shannon Index')
theme_bw()
theme(panel.grid = element_blank(),
panel.border = element_blank())
theme(legend.position="none")
But I have some problems:
1st: I have tried to get a legend but making a continuos scale like 
This is certainly a big improvement from using the same plotting code with your unsmoothed data:
