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Alluvial plot editing scales and colors

Time：10-07

I am trying to figure out how can I change the scales of the columns box, making them bigger so I can see clearly the names.

Is also possible to paint the PIK3CA and ESR1 boxes in dark green and light orange, respectively? Thank you so much! Any help is more than welcome.

This is my code and the plot that I have generate:

library(ggalluvial)

ggplot(data = Allu,
       aes(axis1 = Metastasis_Location, axis2 = Gene_mut, y = Freq))  
  geom_alluvium(aes(fill = T0_T2_PD_event),
                curve_type = "quintic")  
  geom_stratum(width = 1/4)  
  geom_text(stat = "stratum", size = 3,
            aes(label = after_stat(stratum)))  
  scale_x_discrete(limits = c("Metastasis_Location", "Gene_mut"),
                   expand = c(0.05, .05))  
  theme_void()

enter image description here

My data:

structure(list(Metastasis_Location = c(1L, 1L, 2L, 2L, 2L, 2L, 
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 
2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 3L, 3L, 3L, 
3L, 3L, 3L, 3L, 3L, 3L, 3L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 
4L, 4L, 4L, 4L, 4L, 4L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 
5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 6L, 6L, 
6L, 6L, 6L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 
7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 
7L, 7L, 7L, 7L, 7L, 7L, 8L, 8L, 9L, 9L, 9L, 10L, 10L, 10L, 10L, 
10L, 10L, 10L, 10L, 10L, 11L, 11L, 11L, 11L, 11L, 11L, 11L), 
    T0_T2_THERAPY_COD = structure(c(2L, 2L, 1L, 1L, 1L, 1L, 1L, 
    1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 
    1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 
    2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 
    1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 1L, 2L, 2L, 2L, 2L, 
    2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 2L, 2L, 
    2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 
    2L, 2L, 2L, 1L, 1L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 
    2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 
    2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 
    2L, 2L, 2L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 1L, 2L, 2L, 
    2L, 2L, 2L, 2L), .Label = c("A", "F"), class = "factor"), 
    T0_T2_PD_event = structure(c(2L, 2L, 1L, 1L, 1L, 2L, 2L, 
    2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 
    2L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 
    2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 
    2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 
    2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 2L, 
    2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 
    2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 
    1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 
    2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 
    2L, 2L, 2L, 1L, 2L, 2L, 2L, 1L, 2L, 2L, 2L, 2L, 1L, 1L, 2L, 
    2L, 2L, 2L, 2L), .Label = c("No Progression", "Progression"
    ), class = "factor"), Gene_mut = structure(c(4L, 5L, 1L, 
    3L, 4L, 1L, 2L, 3L, 3L, 3L, 3L, 3L, 4L, 4L, 4L, 4L, 4L, 4L, 
    4L, 5L, 5L, 5L, 6L, 3L, 6L, 6L, 6L, 3L, 3L, 3L, 3L, 3L, 3L, 
    3L, 3L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 5L, 5L, 5L, 
    5L, 5L, 6L, 2L, 3L, 4L, 4L, 3L, 3L, 3L, 4L, 5L, 6L, 3L, 6L, 
    3L, 3L, 3L, 3L, 4L, 4L, 4L, 4L, 4L, 5L, 5L, 5L, 6L, 3L, 4L, 
    4L, 5L, 6L, 1L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 4L, 4L, 4L, 4L, 
    4L, 4L, 5L, 5L, 5L, 5L, 5L, 3L, 4L, 3L, 4L, 5L, 6L, 3L, 3L, 
    4L, 5L, 6L, 6L, 6L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 4L, 4L, 
    4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 5L, 5L, 5L, 5L, 5L, 5L, 6L, 
    6L, 6L, 3L, 4L, 3L, 4L, 5L, 6L, 3L, 4L, 5L, 6L, 3L, 4L, 5L, 
    6L, 1L, 6L, 3L, 3L, 4L, 4L, 5L), .Label = c("AKT1", "ERBB2", 
    "ESR1", "PIK3CA", "TP53", "WT"), class = "factor"), LABO_ID = structure(c(45L, 
    8L, 13L, 11L, 11L, 26L, 7L, 15L, 23L, 26L, 35L, 39L, 7L, 
    19L, 26L, 32L, 33L, 35L, 39L, 15L, 19L, 35L, 1L, 37L, 34L, 
    43L, 47L, 3L, 10L, 18L, 20L, 28L, 31L, 36L, 42L, 9L, 10L, 
    14L, 18L, 20L, 28L, 31L, 36L, 44L, 45L, 8L, 10L, 18L, 28L, 
    42L, 2L, 7L, 39L, 7L, 39L, 3L, 4L, 42L, 5L, 42L, 6L, 21L, 
    1L, 10L, 22L, 28L, 46L, 9L, 10L, 14L, 28L, 46L, 10L, 28L, 
    48L, 25L, 23L, 32L, 33L, 40L, 43L, 24L, 3L, 18L, 24L, 28L, 
    31L, 36L, 42L, 18L, 27L, 28L, 31L, 36L, 45L, 18L, 24L, 27L, 
    28L, 42L, 16L, 16L, 18L, 18L, 18L, 29L, 23L, 39L, 39L, 40L, 
    1L, 12L, 47L, 3L, 18L, 20L, 28L, 31L, 36L, 38L, 42L, 5L, 
    18L, 20L, 27L, 28L, 31L, 36L, 38L, 41L, 45L, 8L, 18L, 27L, 
    28L, 42L, 48L, 6L, 17L, 30L, 31L, 31L, 18L, 18L, 18L, 29L, 
    39L, 39L, 40L, 43L, 31L, 31L, 48L, 30L, 13L, 34L, 18L, 36L, 
    18L, 36L, 18L), .Label = c("ER-11", "ER-19", "ER-21", "ER-22", 
    "ER-29", "ER-30", "ER-31", "ER-32", "ER-33", "ER-38", "ER-40", 
    "ER-43", "ER-49", "ER-8", "ER-AZ-04", "ER-AZ-05", "ER-AZ-06", 
    "ER-AZ-07", "ER-AZ-08", "ER-AZ-10", "ER-AZ-11", "ER-AZ-11=ER-47", 
    "ER-AZ-13", "ER-AZ-14", "ER-AZ-15", "ER-AZ-16", "ER-AZ-17", 
    "ER-AZ-18", "ER-AZ-20", "ER-AZ-20=ER-27", "ER-AZ-21", "ER-AZ-23", 
    "ER-AZ-23=ER-52", "ER-AZ-24", "ER-AZ-29", "ER-AZ-31", "ER-AZ-33", 
    "ER-AZ-35", "ER-AZ-37", "ER-AZ-38", "ER-AZ-39", "ER-AZ-40", 
    "ER-AZ-43", "ER-AZ-44", "ER-AZ-45", "ER-AZ-49", "ER-AZ-51", 
    "ER-AZ-53"), class = "factor"), Freq = 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, 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)), class = c("grouped_df", "tbl_df", 
"tbl", "data.frame"), row.names = c(NA, -161L), groups = structure(list(
    Metastasis_Location = c(1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 
    2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 
    4L, 4L, 4L, 4L, 4L, 4L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 5L, 6L, 
    6L, 6L, 6L, 6L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 8L, 
    8L, 9L, 9L, 9L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 10L, 
    11L, 11L, 11L, 11L, 11L), T0_T2_THERAPY_COD = structure(c(2L, 
    2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 
    2L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 1L, 1L, 2L, 2L, 2L, 2L, 1L, 
    1L, 1L, 2L, 2L, 2L, 2L, 2L, 1L, 1L, 2L, 2L, 2L, 1L, 1L, 1L, 
    1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 1L, 1L, 
    1L, 2L, 2L, 2L, 2L, 2L, 1L, 2L, 2L, 2L, 2L), .Label = c("A", 
    "F"), class = "factor"), T0_T2_PD_event = structure(c(2L, 
    2L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 1L, 2L, 2L, 2L, 
    2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 
    2L, 2L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 2L, 2L, 
    2L, 2L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 2L, 2L, 
    2L, 1L, 2L, 2L, 2L, 2L, 1L, 1L, 2L, 2L, 2L), .Label = c("No Progression", 
    "Progression"), class = "factor"), Gene_mut = structure(c(4L, 
    5L, 1L, 3L, 4L, 1L, 2L, 3L, 4L, 5L, 6L, 3L, 6L, 3L, 4L, 5L, 
    6L, 2L, 3L, 4L, 3L, 4L, 5L, 6L, 3L, 6L, 3L, 4L, 5L, 6L, 3L, 
    4L, 5L, 6L, 1L, 3L, 4L, 5L, 3L, 4L, 3L, 4L, 5L, 6L, 3L, 4L, 
    5L, 6L, 6L, 3L, 4L, 5L, 6L, 3L, 4L, 3L, 4L, 5L, 6L, 3L, 4L, 
    5L, 6L, 3L, 4L, 5L, 6L, 1L, 6L, 3L, 4L, 5L), .Label = c("AKT1", 
    "ERBB2", "ESR1", "PIK3CA", "TP53", "WT"), class = "factor"), 
    .rows = structure(list(1L, 2L, 3L, 4L, 5L, 6L, 7L, 8:12, 
        13:19, 20:22, 23L, 24L, 25:27, 28:35, 36:45, 46:50, 51L, 
        52L, 53L, 54:55, 56:58, 59L, 60L, 61L, 62L, 63L, 64:67, 
        68:72, 73:75, 76L, 77L, 78:79, 80L, 81L, 82L, 83:89, 
        90:95, 96:100, 101L, 102L, 103L, 104L, 105L, 106L, 107:108, 
        109L, 110L, 111:112, 113L, 114:121, 122:131, 132:137, 
        138:140, 141L, 142L, 143L, 144L, 145L, 146L, 147L, 148L, 
        149L, 150L, 151L, 152L, 153L, 154L, 155L, 156L, 157:158, 
        159:160, 161L), ptype = integer(0), class = c("vctrs_list_of", 
    "vctrs_vctr", "list"))), class = c("tbl_df", "tbl", "data.frame"
), row.names = c(NA, -72L), .drop = TRUE))

CodePudding user response：

Here is a way you can get the colors - although someone will probably propose a more elegant way of writing it. You can change the colors in the first line of code if you don't like them.

library(ggalluvial)
library(ggplot2)  

  colorfill <- c("white", "white", "white", "white", "white", "white", "white", "white", "white", "white", "white", "white", "white", "darkgreen", "orange", "white", "white")
    
    ggplot(data = Allu,
           aes(axis1 = Metastasis_Location, axis2 = Gene_mut, y = Freq))  
      geom_alluvium(aes(fill = T0_T2_PD_event),
                    curve_type = "quintic")  
      geom_stratum(width = 1/4, fill = colorfill)  
      geom_text(stat = "stratum", size = 3,
                aes(label = after_stat(stratum)))  
      scale_x_discrete(limits = c("Metastasis_Location", "Gene_mut"),
                       expand = c(0.05, .05))  
      theme_void()

enter image description here

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