ggplot scale_alpha_manual for both discrete and continuous variables in data

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I have some data which looks like:

         variable      value   rfvalue  stdfvalue mean_value                    model
1 Protocol Active  0.7975318  0.000000 0.00000000  0.8833071 2013-07-24 to 2019-07-22
2 Protocol Active  0.2716946  0.000000 0.00000000  0.3929385 2011-10-12 to 2017-10-10
3            Wind  0.7384344  1.806452 0.07128713  0.2818933 2010-01-01 to 2015-12-31
4 Protocol Active  1.2555754  0.000000 0.00000000  0.8833071 2013-07-24 to 2019-07-22
5 Protocol Active  0.8638037  0.000000 0.00000000  0.8833071 2013-07-24 to 2019-07-22
6            Wind -0.4009561 13.419355 0.54027120  0.4125869 2013-07-24 to 2019-07-22

I can use the following to plot the data:

d %>% 
  ggplot() +
  coord_flip() +
  ggforce::geom_sina(aes(
    x = variable,
    y = value,
    color = stdfvalue,
    alpha = value),
    method = "counts", maxwidth = 1, size = 1) +
  facet_wrap(~model) +
  scale_color_gradient(
    low = "darkblue",
    high = "darkred",
    breaks = c(0, 1),
    labels = c("     Low", "     High"), 
    guide = guide_colorbar(barwidth = 12, barheight = 0.3))

However, on my full data set the plot looks like:

enter image description here

(Where I changed the darkblue to yellow). The Wind variable looks fine and it is a continuous variable however the Protocol Active variable "hides" some of the data I want to show. It is a discrete variable of (0,1) and I want to put more emphasis on the values with 1. I try to add scale_alpha_manual(values = c(1, 0.1), guide = FALSE) which returns an error. I also cannot seem to get scale_alpha_manual to work with both discrete and continuous.

One attempt was to create two geom_sina plots and filter them according to the two variables - I hoped to apply different alpha values to each of them. I could not get this to work.

 ggplot() +
  coord_flip() +
  ggforce::geom_sina(aes(
    x = variable,
    y = value,
    color = stdfvalue),
    method = "counts", maxwidth = 1, size = 1, data = d %>% filter(variable == "Protocol Active")
  ) +
  ggforce::geom_sina(aes(
    x = variable,
    y = value,
    color = stdfvalue,
    alpha = 0.1),
    method = "counts", maxwidth = 1, size = 1, data = d %>% 
      filter(variable == "Wind")
  ) +
  facet_wrap(~model) +
  scale_color_gradient(
    low = "yellow",
    high = "blue1",
    breaks = c(0, 1),
    labels = c("     Low", "     High"), 
    guide = guide_colorbar(barwidth = 12, barheight = 0.3))

My question is, how can I set the alpha of the discrete variable so I can show a certain class with a bit more emphasis. It would be interesting to know if we can set scale_alpha_continuous and scale_alpha_discrete on the same plots. I am open to hear about any other work arounds also.

Data:

    d <- structure(list(variable = c("Wind", "Wind", "Wind", "Protocol Active", 
"Protocol Active", "Wind", "Wind", "Wind", "Protocol Active", 
"Protocol Active", "Wind", "Wind", "Wind", "Protocol Active", 
"Wind", "Wind", "Wind", "Wind", "Wind", "Protocol Active", "Protocol Active", 
"Wind", "Protocol Active", "Protocol Active", "Protocol Active", 
"Protocol Active", "Wind", "Protocol Active", "Wind", "Wind", 
"Protocol Active", "Protocol Active", "Wind", "Protocol Active", 
"Wind", "Protocol Active", "Wind", "Protocol Active", "Protocol Active", 
"Protocol Active", "Protocol Active", "Wind", "Protocol Active", 
"Protocol Active", "Wind", "Protocol Active", "Wind", "Wind", 
"Protocol Active", "Wind", "Protocol Active", "Wind", "Protocol Active", 
"Protocol Active", "Wind", "Wind", "Wind", "Protocol Active", 
"Wind", "Protocol Active", "Protocol Active", "Protocol Active", 
"Protocol Active", "Protocol Active", "Wind", "Protocol Active", 
"Protocol Active", "Wind", "Wind", "Wind", "Protocol Active", 
"Protocol Active", "Wind", "Protocol Active", "Protocol Active", 
"Wind", "Protocol Active", "Protocol Active", "Wind", "Wind", 
"Wind", "Wind", "Protocol Active", "Wind", "Protocol Active", 
"Wind", "Wind", "Protocol Active", "Protocol Active", "Wind", 
"Protocol Active", "Wind", "Protocol Active", "Wind", "Wind", 
"Protocol Active", "Protocol Active", "Wind", "Protocol Active", 
"Wind", "Protocol Active", "Protocol Active", "Protocol Active", 
"Wind", "Wind", "Wind", "Wind", "Wind", "Protocol Active", "Wind", 
"Protocol Active", "Protocol Active", "Protocol Active", "Wind", 
"Protocol Active", "Wind", "Wind", "Protocol Active", "Wind", 
"Wind", "Wind", "Wind", "Protocol Active", "Wind", "Protocol Active", 
"Protocol Active", "Protocol Active", "Protocol Active", "Wind", 
"Wind", "Protocol Active", "Wind", "Wind", "Protocol Active", 
"Protocol Active", "Wind", "Wind", "Wind", "Wind", "Protocol Active", 
"Wind", "Protocol Active", "Protocol Active", "Protocol Active", 
"Protocol Active", "Wind", "Wind", "Protocol Active", "Wind", 
"Wind", "Protocol Active", "Wind", "Wind", "Protocol Active", 
"Wind", "Protocol Active", "Wind", "Wind", "Protocol Active", 
"Wind", "Protocol Active", "Protocol Active", "Wind", "Wind", 
"Wind", "Wind", "Protocol Active", "Wind", "Protocol Active", 
"Protocol Active", "Protocol Active", "Protocol Active", "Wind", 
"Wind", "Wind", "Wind", "Wind", "Protocol Active", "Protocol Active", 
"Wind", "Wind", "Wind", "Protocol Active", "Wind", "Protocol Active", 
"Wind", "Protocol Active", "Wind", "Wind", "Wind", "Protocol Active", 
"Protocol Active", "Protocol Active", "Protocol Active", "Wind", 
"Wind", "Protocol Active", "Protocol Active", "Wind", "Protocol Active"
), value = c(-0.0989474654197693, 0.629822552204132, -0.0962040945887566, 
1.29249930381775, 0, 0.434465348720551, -0.28844028711319, 0.217110589146614, 
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0.845123291015625, 0, -0.398098558187485, -0.275375932455063, 
0.623717963695526, 0.767583787441254, -0.220980376005173, 0, 
0.856497704982758, -0.0572838261723518, 0, 0, 0.503492951393127, 
0.283374071121216, -0.0997775197029114, 0, -0.185573473572731, 
0.541458964347839, 0.828957080841064, 0.298303335905075, -0.0101631181314588, 
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0.826459050178528, 0.250531941652298, 0, -0.297038346529007, 
0.415378659963608, 0, -0.242933213710785, 0.753650367259979, 
-0.161409094929695, -0.752240180969238, 0, 0.736700534820557, 
0, -0.0983792245388031, 1.13214647769928, 0.286624670028687, 
0.849360644817352, 0.906382441520691, 0.768399834632874, 0.542866706848145, 
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0.487868845462799, -0.336384683847427, 0.365867704153061, 0.458498805761337, 
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1.27674341201782, -0.402126729488373, 1.35678279399872, 0, -0.0197668727487326, 
0.977747678756714, 0.666797459125519, -0.267341256141663, 0.655228078365326, 
0.0420738272368908, 0.430610090494156, 0, -0.122896425426006, 
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0.626144170761108, 0.507866978645325, 0.529027938842773, -0.101144313812256, 
0, 0.777739226818085, 0, -0.414799422025681, 1.35438084602356, 
0.860056400299072, 0.590310633182526, 0.667994678020477, 0.537133276462555, 
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0, -0.550533652305603, 0, 0.5471071600914, 1.18974375724792, 
0.381776362657547, 0.682958662509918, -0.35002875328064, -0.254838764667511, 
0.856454491615295, 0.0177191141992807, 0.781686365604401, 0.759931743144989, 
1.08820796012878, 0.626882433891296, -0.242740288376808, 0.770202159881592, 
0.904597997665405, 0.892723023891449, -0.386538952589035, 0, 
-0.393929898738861, -0.103308126330376, -0.377305179834366, 0.483622252941132, 
0.743905782699585, 0.778063476085663, 0, -0.440237790346146, 
-0.12215880304575, 0.73518306016922, 0, -0.288508862257004, 1.30829179286957
), rfvalue = c(3.96153846153846, 2.03703703703704, 4.83870967741935, 
0, 0, 2.48387096774194, 12.4117647058824, 2.87096774193548, 0, 
0, 3.1875, 4.375, 3.11538461538462, 0, 11.3636363636364, 8.20833333333333, 
0.653846153846154, 0.935483870967742, 4.51612903225806, 0, 0, 
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0, 0, 3.7, 0, 7.58064516129032, 0, 1.96551724137931, 0, 0, 0, 
0, 11.8064516129032, 0, 0, 8.48387096774194, 0, 4.06451612903226, 
24.5, 0, 1.23076923076923, 0, 7.55555555555556, 0, 0, 0.612903225806452, 
0.566666666666667, 2.07142857142857, 0, 10.3548387096774, 0, 
0, 0, 0, 0, 5.55555555555556, 0, 0, 10.6363636363636, 2.2, 2.87096774193548, 
0, 0, 12.9259259259259, 0, 0, 3.73076923076923, 0, 0, 8.83870967741935, 
1.07407407407407, 3.32258064516129, 2.7037037037037, 0, 4.66666666666667, 
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0, 1.96296296296296, 1.88888888888889, 0, 0, 13.6818181818182, 
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5.12121212121212, 15.7741935483871, 3.78787878787879, 7, 0, 7.52, 
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0.807692307692308, 2.72, 6.09677419354839, 0, 0.833333333333333, 
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0, 13.0645161290323, 5.61290322580645, 0, 0, 11.8076923076923, 
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0, 1, 0.099009900990099, 0.505299941758882, 0.113583763574862, 
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1, 0.457029590825428, 0.329599628113069, 0.0233611779697013, 
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0.427867782327458, 0.0859691349285006, 0.113138436102725, 0, 
0, 0.520531807102337, 0, 1, 0.15003808073115, 0, 0, 0.355112456234051, 
0.0403773446389898, 0.133333333333333, 0.108006356191175, 1, 
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), model = c("2013-07-24 to 2019-07-22", "2011-10-12 to 2017-10-10", 
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"2010-01-01 to 2015-12-31", "2011-10-12 to 2017-10-10", "2010-01-01 to 2015-12-31", 
"2011-10-12 to 2017-10-10", "2013-07-24 to 2019-07-22", "2011-10-12 to 2017-10-10", 
"2013-07-24 to 2019-07-22", "2010-01-01 to 2015-12-31", "2013-07-24 to 2019-07-22", 
"2010-01-01 to 2015-12-31", "2010-01-01 to 2015-12-31", "2013-07-24 to 2019-07-22", 
"2011-10-12 to 2017-10-10", "2011-10-12 to 2017-10-10", "2010-01-01 to 2015-12-31", 
"2013-07-24 to 2019-07-22", "2011-10-12 to 2017-10-10", "2013-07-24 to 2019-07-22", 
"2010-01-01 to 2015-12-31", "2011-10-12 to 2017-10-10", "2010-01-01 to 2015-12-31", 
"2013-07-24 to 2019-07-22", "2011-10-12 to 2017-10-10", "2013-07-24 to 2019-07-22", 
"2011-10-12 to 2017-10-10", "2011-10-12 to 2017-10-10", "2011-10-12 to 2017-10-10", 
"2013-07-24 to 2019-07-22", "2013-07-24 to 2019-07-22", "2013-07-24 to 2019-07-22", 
"2013-07-24 to 2019-07-22", "2011-10-12 to 2017-10-10", "2013-07-24 to 2019-07-22", 
"2010-01-01 to 2015-12-31", "2010-01-01 to 2015-12-31", "2013-07-24 to 2019-07-22", 
"2011-10-12 to 2017-10-10", "2011-10-12 to 2017-10-10", "2013-07-24 to 2019-07-22", 
"2010-01-01 to 2015-12-31", "2010-01-01 to 2015-12-31", "2010-01-01 to 2015-12-31", 
"2010-01-01 to 2015-12-31", "2011-10-12 to 2017-10-10", "2011-10-12 to 2017-10-10", 
"2011-10-12 to 2017-10-10", "2010-01-01 to 2015-12-31", "2010-01-01 to 2015-12-31", 
"2013-07-24 to 2019-07-22", "2013-07-24 to 2019-07-22", "2013-07-24 to 2019-07-22", 
"2013-07-24 to 2019-07-22", "2011-10-12 to 2017-10-10", "2011-10-12 to 2017-10-10", 
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"2010-01-01 to 2015-12-31", "2013-07-24 to 2019-07-22", "2010-01-01 to 2015-12-31", 
"2011-10-12 to 2017-10-10", "2013-07-24 to 2019-07-22", "2011-10-12 to 2017-10-10", 
"2011-10-12 to 2017-10-10", "2010-01-01 to 2015-12-31", "2010-01-01 to 2015-12-31", 
"2011-10-12 to 2017-10-10", "2010-01-01 to 2015-12-31", "2013-07-24 to 2019-07-22", 
"2010-01-01 to 2015-12-31", "2010-01-01 to 2015-12-31", "2010-01-01 to 2015-12-31", 
"2010-01-01 to 2015-12-31", "2010-01-01 to 2015-12-31", "2013-07-24 to 2019-07-22", 
"2011-10-12 to 2017-10-10", "2010-01-01 to 2015-12-31", "2013-07-24 to 2019-07-22", 
"2011-10-12 to 2017-10-10", "2013-07-24 to 2019-07-22", "2011-10-12 to 2017-10-10", 
"2013-07-24 to 2019-07-22", "2013-07-24 to 2019-07-22", "2011-10-12 to 2017-10-10", 
"2011-10-12 to 2017-10-10", "2010-01-01 to 2015-12-31", "2011-10-12 to 2017-10-10", 
"2010-01-01 to 2015-12-31", "2011-10-12 to 2017-10-10", "2013-07-24 to 2019-07-22", 
"2013-07-24 to 2019-07-22", "2013-07-24 to 2019-07-22", "2010-01-01 to 2015-12-31", 
"2010-01-01 to 2015-12-31", "2011-10-12 to 2017-10-10", "2011-10-12 to 2017-10-10", 
"2011-10-12 to 2017-10-10", "2010-01-01 to 2015-12-31", "2010-01-01 to 2015-12-31", 
"2011-10-12 to 2017-10-10", "2010-01-01 to 2015-12-31", "2010-01-01 to 2015-12-31", 
"2011-10-12 to 2017-10-10", "2010-01-01 to 2015-12-31", "2013-07-24 to 2019-07-22", 
"2013-07-24 to 2019-07-22", "2011-10-12 to 2017-10-10", "2010-01-01 to 2015-12-31", 
"2010-01-01 to 2015-12-31", "2010-01-01 to 2015-12-31", "2013-07-24 to 2019-07-22", 
"2010-01-01 to 2015-12-31", "2013-07-24 to 2019-07-22", "2011-10-12 to 2017-10-10", 
"2013-07-24 to 2019-07-22", "2010-01-01 to 2015-12-31", "2013-07-24 to 2019-07-22", 
"2011-10-12 to 2017-10-10", "2013-07-24 to 2019-07-22", "2013-07-24 to 2019-07-22", 
"2010-01-01 to 2015-12-31", "2013-07-24 to 2019-07-22", "2010-01-01 to 2015-12-31", 
"2010-01-01 to 2015-12-31", "2010-01-01 to 2015-12-31", "2011-10-12 to 2017-10-10", 
"2013-07-24 to 2019-07-22", "2011-10-12 to 2017-10-10", "2013-07-24 to 2019-07-22", 
"2013-07-24 to 2019-07-22", "2010-01-01 to 2015-12-31", "2011-10-12 to 2017-10-10", 
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"2011-10-12 to 2017-10-10", "2010-01-01 to 2015-12-31", "2013-07-24 to 2019-07-22", 
"2010-01-01 to 2015-12-31", "2013-07-24 to 2019-07-22", "2013-07-24 to 2019-07-22"
)), row.names = c(NA, -200L), class = "data.frame")
ggplot2 r
1 Answers

One option to achieve your desired result would be by scale_alpha_identity. As an example I added a variable alpha to your dataset which defines the mapping (or the breaks) from value to specific alpha levels. This new variable is then mapped on the alpha aesthetic inside ggplot. By default no legend will show up, so that you have to set-up it up manually by specifying the desired breaks and labels.

Concerning your second question. As far as I know, it is not possible to mix scale_xxx_discrete and scale_xxx_continuous. You can map different variables to the same scale, but there is only scale per aestheic and either is it discrete or continuous. If you want to achieve more control over the scales you have to make two plots and glue them together e.g. by patchwork.

# Packages
library(ggplot2)
library(ggforce)
library(dplyr)

# Plot

d %>%
  mutate(alpha = case_when(
    variable == "Wind" ~ ifelse(value > 1, 1, 0.5),
    TRUE ~ ifelse(value > 0, 1, .2)
  )) %>%
  ggplot() +
  coord_flip() +
  ggforce::geom_sina(aes(
    x = variable,
    y = value,
    color = stdfvalue,
    alpha = alpha
  ),
  method = "counts", maxwidth = 1, size = 1
  ) +
  facet_wrap(~model) +
  scale_color_gradient(
    low = "yellow",
    high = "darkred",
    breaks = c(0, 1),
    labels = c("     Low", "     High"),
    guide = guide_colorbar(barwidth = 12, barheight = 0.3)
  ) +
  scale_alpha_identity(breaks = c(.2, .5, 1), labels = c("One", "Two", "Three"), guide = "legend") +
  theme(legend.position = "bottom")

Created on 2020-03-15 by the reprex package (v0.3.0)

user_129938610
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