Ordering for stacked bar chart but with different values in each one.

tidyverse
,
1

Hi, Im want make order between the most highest values, but dont find the exactly form. In this community exist other responses about this topic, but not function for my case. Im try with order() and reorder()

ggplot(d3) + 
  geom_bar(aes(x=Patient, y=`Relative abundance`,fill=Phylum), position="fill", stat="identity") +     scale_x_discrete("Pacientes") + 
  scale_y_continuous("Abundancia relativa",labels=scales::percent) +
  labs(title = "Grupo Neumonia",subtitle = "Abundancia relativa de filo") +
  theme_classic()+ scale_fill_manual(values=c ("Grey", "Green", "Red", "Blue2", "Purple","Orange","yellow3","turquoise1", "black","green4","magenta","Purple4","Pink2","Brown","green2"))

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image689Ɨ425 21.3 KB

I am looking for a graph with this order, from highest to lowest in each Paciente

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image594Ɨ340 62.5 KB

structure(list(Group = c("CAP", "CAP", "CAP", "CAP", "CAP", "CAP", 
"CAP", "CAP", "CAP", "CAP", "CAP", "CAP", "CAP", "CAP", "CAP", 
"CAP", "CAP", "CAP", "CAP", "CAP", "CAP", "CAP", "CAP", "CAP", 
"CAP", "CAP", "CAP", "CAP", "CAP", "CAP", "CAP", "CAP", "CAP", 
"CAP", "CAP", "CAP", "CAP", "CAP", "CAP", "CAP", "CAP", "CAP", 
"CAP", "CAP", "CAP", "CAP", "CAP", "CAP", "CAP", "CAP", "CAP", 
"CAP", "CAP", "CAP", "CAP", "CAP", "CAP", "CAP", "CAP", "CAP", 
"CAP", "CAP", "CAP", "CAP", "CAP", "CAP", "CAP", "CAP", "CAP", 
"CAP"), Phylum = structure(c(1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 
2L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 4L, 4L, 5L, 6L, 6L, 6L, 
6L, 6L, 6L, 6L, 6L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 7L, 8L, 8L, 
8L, 8L, 8L, 8L, 8L, 8L, 8L, 9L, 9L, 9L, 9L, 10L, 10L, 11L, 11L, 
11L, 11L, 11L, 11L, 11L, 11L, 11L, 12L, 12L, 12L, 12L, 12L, 12L, 
12L, 12L), .Label = c("Acidobacteria", "Actinobacteria", "Bacteroidetes", 
"Chloroflexi", "Deinococcus-Thermus", "Epsilonbacteraeota", "Firmicutes", 
"Fusobacteria", "Otros", "Patescibacteria", "Proteobacteria", 
"Spirochaetes", "Synergistetes", "Tenericutes", "Verrucomicrobia"
), class = "factor"), `Sample  type` = c(3, 3, 4, 5, 5, 5, 5, 
5, 5, 3, 3, 4, 5, 5, 5, 5, 5, 5, 5, 5, 5, 3, 4, 5, 5, 5, 5, 5, 
5, 3, 3, 4, 5, 5, 5, 5, 5, 5, 3, 3, 4, 5, 5, 5, 5, 5, 5, 3, 3, 
4, 5, 5, 5, 3, 3, 4, 5, 5, 5, 5, 5, 5, 3, 3, 4, 5, 5, 5, 5, 5
), Patient = c("5-003", "5-002", "5-002", "5-001", "5-002", "5-003", 
"5-005", "5-006", "5-007", "5-002", "5-003", "5-002", "5-001", 
"5-002", "5-003", "5-005", "5-006", "5-007", "5-005", "5-006", 
"5-007", "5-002", "5-002", "5-001", "5-002", "5-003", "5-005", 
"5-006", "5-007", "5-002", "5-003", "5-002", "5-001", "5-002", 
"5-003", "5-005", "5-006", "5-007", "5-002", "5-003", "5-002", 
"5-001", "5-002", "5-003", "5-005", "5-006", "5-007", "5-002", 
"5-003", "5-002", "5-001", "5-002", "5-003", "5-002", "5-003", 
"5-002", "5-001", "5-002", "5-003", "5-005", "5-006", "5-007", 
"5-002", "5-003", "5-002", "5-001", "5-002", "5-003", "5-005", 
"5-006"), `Relative abundance` = c(0.00436022919615096, 0.00433209868520805, 
0.00725767182327063, 0.034150440284692, 0.00469779532746587, 
0.0144872131355983, 0.0917898572067134, 0.010858377223963, 0.322966396135543, 
0.0115897705084787, 0.00185661372223202, 0.044418076778854, 0.0147403877340845, 
0.00886111094701646, 0.054967018382445, 0.0321813045186884, 0.00351631386786368, 
0.00601992934178261, 8.43915328287282e-05, 8.43915328287282e-05, 
0.000112522043771638, 0.00261613751769058, 0.00697636671384153, 
0.0065825395606408, 0.0014909170799742, 0.0318999994092593, 0.0322656960515171, 
0.00241922394109021, 0.0342910928394066, 1.34899865226722, 0.332840205476504, 
1.22834689083308, 2.55183116967508, 0.767653513121055, 1.70487774620597, 
2.93828812900877, 1.9513291525768, 2.18799114113949, 0.0404235442249608, 
0.00101269839394474, 0.187996204631464, 0.0566829795499625, 0.00998633138473284, 
0.201780154993489, 0.327045320222265, 0.0708607570651888, 0.0255425039361617, 
0.00210978832071821, 0.00669506160441244, 0.000393827153200732, 
0.00160343912374584, 0.000225044087543275, 0.00202539678788948, 
1.02566655948942, 0.140202466539461, 1.2134095895224, 0.830890901720715, 
0.0496222213032922, 0.698536847734326, 1.18505403449194, 0.345245760802327, 
0.273653610452623, 0.000112522043771638, 0.00123774248148801, 
8.43915328287282e-05, 8.43915328287282e-05, 0.000168783065657456, 
0.0162031743031158, 0.075446030348883, 0.00666693109346953)), row.names = c(NA, 
-70L), groups = structure(list(Group = c("CAP", "CAP", "CAP", 
"CAP", "CAP", "CAP", "CAP", "CAP", "CAP", "CAP", "CAP", "CAP", 
"CAP", "CAP", "CAP", "CAP", "CAP", "CAP", "CAP", "CAP", "CAP", 
"CAP", "CAP", "CAP", "CAP", "CAP", "CAP", "CAP"), Phylum = structure(c(1L, 
2L, 2L, 2L, 3L, 3L, 3L, 4L, 5L, 6L, 6L, 6L, 7L, 7L, 7L, 8L, 8L, 
8L, 9L, 9L, 9L, 10L, 11L, 11L, 11L, 12L, 12L, 12L), .Label = c("Acidobacteria", 
"Actinobacteria", "Bacteroidetes", "Chloroflexi", "Deinococcus-Thermus", 
"Epsilonbacteraeota", "Firmicutes", "Fusobacteria", "Otros", 
"Patescibacteria", "Proteobacteria", "Spirochaetes", "Synergistetes", 
"Tenericutes", "Verrucomicrobia"), class = "factor"), `Sample  type` = c(3, 
3, 4, 5, 3, 4, 5, 5, 5, 3, 4, 5, 3, 4, 5, 3, 4, 5, 3, 4, 5, 5, 
3, 4, 5, 3, 4, 5), .rows = structure(list(1L, 2L, 3L, 4:9, 10:11, 
    12L, 13:18, 19:20, 21L, 22L, 23L, 24:29, 30:31, 32L, 33:38, 
    39:40, 41L, 42:47, 48:49, 50L, 51L, 52:53, 54:55, 56L, 57:62, 
    63:64, 65L, 66:70), ptype = integer(0), class = c("vctrs_list_of", 
"vctrs_vctr", "list"))), row.names = c(NA, -28L), class = c("tbl_df", 
"tbl", "data.frame"), .drop = TRUE), class = c("grouped_df", 
"tbl_df", "tbl", "data.frame"))

Thanks

2

You need to convert Phylum to a factor, ordered by the mean abundance. I think this will do it.

d3 <- d3 %>% 
  group_by(Phylum) %>% 
  mutate(
    mean = mean(`Relative abundance`)
  ) %>% 
  ungroup() %>% 
  arrange(desc(mean)) %>% 
  mutate(
    Phylum = factor(Phylum, levels = unique(Phylum))
  )
3

Excellent, Im dont know the exactly form, thanks you. The order of colors change but is an excellent plot.

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