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wilkelab / ggridges

Ridgeline plots in ggplot2
https://wilkelab.org/ggridges
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Warning message: Ignoring unknown parameters: quantile_lines, jittered_points. Why? #42

Closed stefanucci-luca closed 5 years ago

stefanucci-luca commented 5 years ago

Hello,

I've been trying to use geom_density_ridges() function but when I use the functions quantile_lines() and jittered_points() I get:

Warning: Ignoring unknown parameters: quantile_lines, jittered_points

I don't know if I have ant problems in package's versions creating conflicts or I am setting something wrong.

Here the data I am using, the plot I am trying to make and SessionInfo()

df_var <- structure(list(Promoter.id1 = c(1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 
1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L), Distance_bait_prey = c(120536, 
118081, 109646, 105159, 97202, 71739, 43239, 42450, 41350, 35391, 
30686, 22941, 2584, 1873, 4264, 10040, 10794, 18074, 32473, 44556, 
292007, 390016, 0, 0, 142512, 131396, 110989, 109562, 104713, 
95261, 86678, 69790, 55695, 35697, 2889, 3958, 38661, 43660, 
44783, 49321, 54148, 99101, 99977, 119272, 1484139, 409111, 386732, 
123910, 118993, 115927, 113762, 79247, 66060, 49530, 40555, 37697, 
30777, 9457, 22946, 36503, 67066, 77248, 205036, 317144, 0, 0, 
685454, 118907, 111509, 82273, 40797, 31511, 2699, 3438, 9215, 
17249, 0, 0, 213732, 94776, 0, 86753, 69263, 67025, 66564, 54178, 
51116, 50332, 43140, 41183, 40896, 34972, 24871, 23565, 10131, 
7517, 24279, 29130, 30790, 33482), node.class2 = c("Intron", 
"Intron", "Intron", "Intron", "Intron", "intergenic_region", 
"Promoter_flanking_region", "Promoter_flanking_region", "Exons", 
"Exons", "Exons", "intergenic_region", "Promoter_flanking_region", 
"Promoter_flanking_region", "Exons", "Promoter", "Promoter", 
"Promoter", "intergenic_region", "Intron", "intergenic_region", 
"Intron", "Intron", "Intron", "Exons", "Intron", "CTCF", "Intron", 
"Intron", "Intron", "Gene_name", "intergenic_region", "intergenic_region", 
"Exons", "Promoter_flanking_region", "Exons", "Promoter_flanking_region", 
"Promoter_flanking_region", "Intron", "Intron", "Exons", "Exons", 
"Intron", "intergenic_region", "Intron", "Enhancer", "Promoter", 
"Intron", "Intron", "Intron", "Intron", "Promoter", "Promoter_flanking_region", 
"Promoter_flanking_region", "Exons", "Exons", "Intron", "Promoter", 
"intergenic_region", "Exons", "Intron", "Exons", "CTCF", "Exons", 
"intergenic_region", "Exons", "Intron", "Intron", "CTCF", "Gene_name", 
"Exons", "Exons", "Promoter_flanking_region", "Exons", "Promoter", 
"Promoter", "Exons", "intergenic_region", "CTCF", "Promoter", 
"Intron", "CTCF", "Promoter", "Promoter", "Promoter", "CTCF", 
"CTCF", "CTCF", "Promoter_flanking_region", "Promoter", "Promoter", 
"Promoter", "CTCF", "CTCF", "Promoter_flanking_region", "Promoter", 
"CTCF", "Promoter", "Promoter", "Promoter")), row.names = c(NA, 
100L), class = "data.frame")

ggplot(df_var, aes(x = log10(Distance_bait_prey), 
                   y = node.class2, 
                   fill = node.class2, 
                   height = ..density..), 
       alpha = 0.7) +
  geom_density_ridges(scale = 4, 
                      stat = "density", 
                      alpha = 0.9,
                      panel_scaling = TRUE,
                      quantile_lines = TRUE,
                      jittered_points = TRUE) +
  scale_x_continuous(limits = c(2,7), 
                     name = "Distance Bait-prey [log10(bp)]", 
                     breaks = seq(2, 7, by = 1)) +
  labs(title = str_sub(name1, 1,-5),
       fill = "Distances grouped by Feature") +
  guides(fill = guide_legend(reverse = TRUE)) +
  theme_classic() +
  theme(plot.title = element_text(size = 54),
        axis.text.x = element_text(angle = 0, size = 16),
        axis.text.y = element_blank(),
        axis.title.y = element_blank(),
        axis.title.x = element_text(size = 0),
        axis.ticks.y = element_blank(),
        legend.title = element_text(size = 30),
        legend.text = element_text(size = 22),
        legend.position = "bottom" ,
        legend.key.size = unit(1, "cm"),
        panel.grid.major = element_line(colour = "grey90",
                                        linetype = "solid",
                                        size = 0.3))

> sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS  10.14.6

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib

locale:
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8

attached base packages:
[1] grid      stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] ggplotify_0.0.3        ggridges_0.5.1         ComplexHeatmap_1.20.0  gridExtra_2.3          gtable_0.3.0           ggraph_1.0.2          
 [7] igraph_1.2.4.1         multipanelfigure_2.0.2 magrittr_1.5           UpSetR_1.4.0           scales_1.0.0           cowplot_0.9.4         
[13] RColorBrewer_1.1-2     pheatmap_1.0.12        plotly_4.9.0           forcats_0.4.0          stringr_1.4.0          dplyr_0.8.0.1         
[19] purrr_0.3.2            readr_1.3.1            tidyr_0.8.3            tibble_2.1.1           ggplot2_3.2.1          tidyverse_1.2.1       

loaded via a namespace (and not attached):
 [1] viridis_0.5.1              httr_1.4.0                 jsonlite_1.6               viridisLite_0.3.0          modelr_0.1.4              
 [6] assertthat_0.2.1           rvcheck_0.1.3              cellranger_1.1.0           yaml_2.2.0                 ggrepel_0.8.1             
[11] pillar_1.4.0               backports_1.1.4            lattice_0.20-38            glue_1.3.1                 digest_0.6.18             
[16] assertive.types_0.0-3      polyclip_1.10-0            rvest_0.3.3                colorspace_1.4-1           htmltools_0.3.6           
[21] plyr_1.8.4                 pkgconfig_2.0.2            GetoptLong_0.1.7           broom_0.5.2                assertive.properties_0.0-4
[26] haven_2.1.0                magick_2.0                 tweenr_1.0.1               ggforce_0.2.2              generics_0.0.2            
[31] farver_1.1.0               withr_2.1.2                lazyeval_0.2.2             cli_1.1.0                  crayon_1.3.4              
[36] readxl_1.3.1               assertive.numbers_0.0-2    nlme_3.1-139               MASS_7.3-51.4              xml2_1.2.0                
[41] tools_3.5.1                data.table_1.12.2          hms_0.4.2                  GlobalOptions_0.1.0        assertive.files_0.0-2     
[46] munsell_0.5.0              compiler_3.5.1             gridGraphics_0.4-1         rlang_0.3.4                rstudioapi_0.10           
[51] circlize_0.4.6             rjson_0.2.20               htmlwidgets_1.3            assertive.base_0.0-7       labeling_0.3              
[56] codetools_0.2-16           R6_2.4.0                   lubridate_1.7.4            shape_1.4.4                stringi_1.4.3             
[61] Rcpp_1.0.1                 tidyselect_0.2.5
clauswilke commented 5 years ago

These are parameters of stat_density_ridges() but you're using stat_density().