lefse analysis questions and plotting without tags

[Roctry]

Hello, microeco has very conveniently implemented lefse analysis, but I have the following two questions.

First
t1 <- trans_diff$new(dataset = dataset, method = “lefse”, group = “Group”, alpha = 0.05, lefse_norm = 10000,
taxa_level = “all”, p_adjust_method = “none”, boots = 100, by_group = “KW”,
lefse_subgroup = NULL)
t1$plot_diff_bar(threshold = 2,
width = 0.8, group_order = c(“RR”, “RW”), add_sig = T,
use_number = 1:20)
Why is it that the LDA in t1$res_diff are all greater than zero, but in t1$plot_diff_bar out of the plot there is a negative LDA score value.

Second
t1$plot_diff_cladogram(use_taxa_num = 200,
use_feature_num = 30,
clade_label_level = 5,
group_order = c(“RR”, “RW”),
select_show_labels = NULL ,
only_select_show = F,
sep = “|”,
branch_size = 3,
alpha = 0.2,
clade_label_size = 2)
The outgoing developmental tree has no species annotations and no letters (a, b, c ···), but the labeling is normal.

Very much looking forward to getting an answer.

[ChiLiubio]

Hi. It is not negative values in the figure, just for the beauty with two types of values on both sides. For the second issue, please refer to this topic (https://chiliubio.github.io/microeco_tutorial/other-examples-1.html#tidy_taxonomy-function) and use tidy_taxonomy function to tidy your taxonomic info. It is also mentioned in the trans_diff part (https://chiliubio.github.io/microeco_tutorial/model-based-class.html#trans_diff-class)

meco_qiime2$tax_table %<>% tidy_taxonomy
meco_qiime2$tidy_dataset()
meco_qiime2$cal_abund()
lefse_diff <- trans_diff$new(dataset = meco_qiime2, method = "lefse", group = "Group")

[Roctry]

rm(list = ls())
sample_info_16S <- read.xlsx("sample_info_16S.xlsx", rowNames = TRUE)
otu_table_16S <- read.xlsx("otu_table_16S.xlsx", rowNames = TRUE)
taxonomy_table_16S <- read.xlsx("taxonomy_table_16S.xlsx",rowNames = TRUE)
dataset <- microtable$new(sample_table = sample_info_16S, otu_table = otu_table_16S,
tax_table = taxonomy_table_16S)
dataset$tax_table %<>% tidy_taxonomy
dataset
t1 <- trans_diff$new(dataset = dataset, method = "lefse", group = "Group", alpha = 0.05, lefse_norm = 10000,
taxa_level = "all", p_adjust_method = "none", boots = 100, by_group = "KW",
lefse_subgroup = NULL)
t1$plot_diff_cladogram(use_taxa_num = 200,
use_feature_num = 30,
clade_label_level = 5,
group_order = c("RR", "RW"),
select_show_labels = NULL ,
only_select_show = F,
sep = "|",
branch_size = 3,
alpha = 0.2,
clade_label_size = 2)

Hello, I used tidy_taxonomy and still did not solve the problem.

[ChiLiubio]

Hi. Could you please attach your dataset object so that I can reproduce your issue? To save the dataset, please follow the steps in the tutorial (https://chiliubio.github.io/microeco_tutorial/notes.html#save-function) and attach the compressed object.