Delete or avoid a specific datum on the x-axis with ggplot2

tidyverse
,
1

Hi Community

I want to eliminate the patient (4-012) with this interaction (0 Admission with Induced Sputum) on the x-axis, since it does not exist in the database. Only is this value not in the interaction, because in the other events it does exist.

image

d1 <- d %>% 
  group_by(Phylum) %>% 
  mutate(
    mean = mean(`Relative abundance`)
  ) %>% 
  ungroup() %>% 
  arrange(desc(mean)) %>% 
  mutate(
    Phylum = factor(Phylum, levels = unique(Phylum)) # maybe this es the problem 
  )
ggplot(d1) + 
  geom_bar(aes(x=Patient, y=`Relative abundance`,fill=Phylum), position="fill", stat="identity") +     scale_x_discrete("Patients") + 
  scale_y_continuous("Relative abundance",labels=scales::percent) +
  labs(title = "Relative abundance of phylum by sample type") +
  theme_classic() + 
  scale_fill_manual(values=c ("#FC000D", "#30E500", "#E10072", "#B58E2C","#10A542","#730183","#800009",
  "#6C2914", "#01020D","#00B9B9"))+
    facet_grid(~`Time point`+ `Sample  type`)+
  theme(axis.text.x = element_text(angle = 90, vjust = 0.5, hjust=1))

d<-structure(list(Group = c("HIV+CAP", "HIV+CAP", "HIV+CAP", "HIV+CAP", 
"HIV+CAP", "HIV+CAP", "HIV+CAP", "HIV+CAP", "HIV+CAP", "HIV+CAP", 
"HIV+CAP", "HIV+CAP", "HIV+CAP", "HIV+CAP", "HIV+CAP", "HIV+CAP", 
"HIV+CAP", "HIV+CAP", "HIV+CAP", "HIV+CAP", "HIV+CAP", "HIV+CAP", 
"HIV+CAP", "HIV+CAP", "HIV+CAP", "HIV+CAP", "HIV+CAP", "HIV+CAP", 
"HIV+CAP", "HIV+CAP", "HIV+CAP", "HIV+CAP", "HIV+CAP", "HIV+CAP", 
"HIV+CAP", "HIV+CAP", "HIV+CAP", "HIV+CAP", "HIV+CAP", "HIV+CAP", 
"HIV+CAP", "HIV+CAP", "HIV+CAP", "HIV+CAP", "HIV+CAP", "HIV+CAP", 
"HIV+CAP", "HIV+CAP", "HIV+CAP", "HIV+CAP", "HIV+CAP", "HIV+CAP", 
"HIV+CAP", "HIV+CAP", "HIV+CAP", "HIV+CAP", "HIV+CAP", "HIV+CAP", 
"HIV+CAP", "HIV+CAP", "HIV+CAP", "HIV+CAP", "HIV+CAP", "HIV+CAP", 
"HIV+CAP", "HIV+CAP", "HIV+CAP", "HIV+CAP"), Patient = c("4-001", 
"4-001", "4-001", "4-012", "4-012", "4-025", "4-025", "4-025", 
"4-001", "4-001", "4-001", "4-012", "4-012", "4-025", "4-025", 
"4-025", "4-001", "4-001", "4-001", "4-012", "4-012", "4-025", 
"4-025", "4-025", "4-001", "4-001", "4-001", "4-012", "4-012", 
"4-025", "4-025", "4-025", "4-001", "4-001", "4-001", "4-012", 
"4-012", "4-025", "4-025", "4-025", "4-001", "4-001", "4-001", 
"4-012", "4-012", "4-025", "4-025", "4-001", "4-012", "4-012", 
"4-025", "4-025", "4-001", "4-001", "4-001", "4-012", "4-012", 
"4-025", "4-001", "4-025", "4-025", "4-001", "4-001", "4-001", 
"4-012", "4-012", "4-025", "4-025"), `Time point` = c("0 Admission", 
"0 Admission", "6 follow-up", "0 Admission", "6 follow-up", "0 Admission", 
"6 follow-up", "0 Admission", "0 Admission", "0 Admission", "6 follow-up", 
"0 Admission", "6 follow-up", "0 Admission", "6 follow-up", "0 Admission", 
"0 Admission", "0 Admission", "6 follow-up", "0 Admission", "6 follow-up", 
"0 Admission", "6 follow-up", "0 Admission", "0 Admission", "0 Admission", 
"6 follow-up", "0 Admission", "6 follow-up", "0 Admission", "6 follow-up", 
"0 Admission", "0 Admission", "0 Admission", "6 follow-up", "0 Admission", 
"6 follow-up", "0 Admission", "6 follow-up", "0 Admission", "0 Admission", 
"0 Admission", "6 follow-up", "0 Admission", "6 follow-up", "6 follow-up", 
"0 Admission", "0 Admission", "0 Admission", "6 follow-up", "6 follow-up", 
"0 Admission", "0 Admission", "0 Admission", "6 follow-up", "0 Admission", 
"6 follow-up", "0 Admission", "6 follow-up", "0 Admission", "0 Admission", 
"0 Admission", "0 Admission", "6 follow-up", "0 Admission", "6 follow-up", 
"6 follow-up", "0 Admission"), `Sample  type` = c("BAL", "Induced Sputum", 
"Induced Sputum", "BAL", "Induced Sputum", "BAL", "Induced Sputum", 
"Induced Sputum", "BAL", "Induced Sputum", "Induced Sputum", 
"BAL", "Induced Sputum", "BAL", "Induced Sputum", "Induced Sputum", 
"BAL", "Induced Sputum", "Induced Sputum", "BAL", "Induced Sputum", 
"BAL", "Induced Sputum", "Induced Sputum", "BAL", "Induced Sputum", 
"Induced Sputum", "BAL", "Induced Sputum", "BAL", "Induced Sputum", 
"Induced Sputum", "BAL", "Induced Sputum", "Induced Sputum", 
"BAL", "Induced Sputum", "BAL", "Induced Sputum", "Induced Sputum", 
"BAL", "Induced Sputum", "Induced Sputum", "BAL", "Induced Sputum", 
"Induced Sputum", "Induced Sputum", "BAL", "BAL", "Induced Sputum", 
"Induced Sputum", "Induced Sputum", "BAL", "Induced Sputum", 
"Induced Sputum", "BAL", "Induced Sputum", "Induced Sputum", 
"Induced Sputum", "BAL", "Induced Sputum", "BAL", "Induced Sputum", 
"Induced Sputum", "BAL", "Induced Sputum", "Induced Sputum", 
"Induced Sputum"), Phylum = structure(c(1L, 1L, 1L, 1L, 1L, 1L, 
1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 3L, 3L, 3L, 3L, 3L, 3L, 
3L, 3L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 4L, 5L, 5L, 5L, 5L, 5L, 5L, 
5L, 5L, 6L, 6L, 6L, 6L, 6L, 6L, 6L, 7L, 7L, 7L, 7L, 7L, 8L, 8L, 
8L, 8L, 8L, 8L, 9L, 9L, 9L, 10L, 10L, 10L, 10L, 10L, 10L, 10L
), .Label = c("Firmicutes", "Proteobacteria", "Fusobacteria", 
"Bacteroidetes", "Epsilonbacteraeota", "Actinobacteria", "Patescibacteria", 
"Spirochaetes", "Otros", "Tenericutes"), class = "factor"), Counting = c(33540, 
29550, 48681, 30346, 59661, 2754, 61297, 23253, 36, 20, 32809, 
48562, 19447, 2, 6316, 39114, 669, 440, 20114, 12788, 3566, 3036, 
1013, 2973, 100, 46, 1222, 25580, 366, 693, 104, 1232, 1936, 
279, 2695, 1173, 3541, 189, 604, 294, 234, 454, 203, 93, 323, 
1770, 82, 5, 413, 4, 57, 26, 15, 43, 11, 270, 16, 4, 44, 104, 
14, 17, 11, 14, 119, 18, 5, 7), `Relative abundance` = c(0.943497337025182, 
0.831256598362973, 1.36942140321177, 0.853648485073529, 1.67829441336492, 
0.0774714271367725, 1.72431592926752, 0.654118770955473, 0.00101269839394474, 
0.000562610218858188, 0.922933933525915, 1.36607387240957, 0.547054046306759, 
5.62610218858188e-05, 0.177672307115416, 1.10029680502096, 0.0188193118208064, 
0.0123774248148801, 0.56581709710568, 0.359732973937926, 0.100313402022415, 
0.085404231222673, 0.0284962075851672, 0.0836320090332697, 0.00281305109429094, 
0.00129400350337383, 0.0343754843722353, 0.719578469919623, 0.0102957670051048, 
0.0194944440834362, 0.00292557313806258, 0.0346567894816644, 
0.0544606691854726, 0.00784841255307172, 0.0758117269911409, 
0.0329970893360327, 0.0996101392488422, 0.00531666656820988, 
0.0169908286095173, 0.00827037021721537, 0.0065825395606408, 
0.0127712519680809, 0.00571049372141061, 0.00261613751769058, 
0.00908615503455974, 0.0497910043689497, 0.00230670189731857, 
0.000140652554714547, 0.0116179010194216, 0.000112522043771638, 
0.00160343912374584, 0.000731393284515645, 0.000421957664143641, 
0.0012096119705451, 0.000309435620372004, 0.00759523795458554, 
0.000450088175086551, 0.000112522043771638, 0.00123774248148801, 
0.00292557313806258, 0.000393827153200732, 0.00047821868602946, 
0.000309435620372004, 0.000393827153200732, 0.00334753080220622, 
0.000506349196972369, 0.000140652554714547, 0.000196913576600366
), mean = c(1.01650304554977, 1.01650304554977, 1.01650304554977, 
1.01650304554977, 1.01650304554977, 1.01650304554977, 1.01650304554977, 
1.01650304554977, 0.514457816751663, 0.514457816751663, 0.514457816751663, 
0.514457816751663, 0.514457816751663, 0.514457816751663, 0.514457816751663, 
0.514457816751663, 0.156824082192852, 0.156824082192852, 0.156824082192852, 
0.156824082192852, 0.156824082192852, 0.156824082192852, 0.156824082192852, 
0.156824082192852, 0.103179197824724, 0.103179197824724, 0.103179197824724, 
0.103179197824724, 0.103179197824724, 0.103179197824724, 0.103179197824724, 
0.103179197824724, 0.0376632378386878, 0.0376632378386878, 0.0376632378386878, 
0.0376632378386878, 0.0376632378386878, 0.0376632378386878, 0.0376632378386878, 
0.0376632378386878, 0.012694897724093, 0.012694897724093, 0.012694897724093, 
0.012694897724093, 0.012694897724093, 0.012694897724093, 0.012694897724093, 
0.00284118160523385, 0.00284118160523385, 0.00284118160523385, 
0.00284118160523385, 0.00284118160523385, 0.00168314223808408, 
0.00168314223808408, 0.00168314223808408, 0.00168314223808408, 
0.00168314223808408, 0.00168314223808408, 0.00151904759091711, 
0.00151904759091711, 0.00151904759091711, 0.000767561084299385, 
0.000767561084299385, 0.000767561084299385, 0.000767561084299385, 
0.000767561084299385, 0.000767561084299385, 0.000767561084299385
)), row.names = c(NA, -68L), class = c("tbl_df", "tbl", "data.frame"
))

Thanks

2

In facet_grid, set scales = "free_x". This allows each sub plot to have its own x axis.

facet_grid(~`Time point`+ `Sample  type`, scales = "free_x")
1 Like
3

Thanks @FJCC , Im going to run the script and put the result, tnks!

Was excellent

The plot

image
image672×576 8.32 KB

4

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