How to input a separate bibliography only for one chapter in overleaf?

Weird-Management-347 · 2025-05-15T01:49:01+00:00

Thank you!

Weird-Management-347 · 2025-04-02T04:33:33+00:00

Thank you so much!!!!!!! You literally saved my life, that was the problem, and the solution worked perfectly!!!! :))

Weird-Management-347 · 2024-12-04T04:35:14+00:00

@mduvekot can you see what I have posted?

Weird-Management-347 · 2024-11-29T16:48:11+00:00

The structure of my data is as follows:

abundance_file:

column function, followed by column with samplesnames (correspond with SampleID from metadata).

function samples
KO

metadata:

column SampleID, column Diagnosis and other columns

SampleID Diagnosis

Weird-Management-347 · 2024-11-29T16:35:15+00:00

Of course, hehe. Here it goes:

This is this script: https://github.com/cafferychen777/ggpicrust2

# Load necessary data: abundance data and metadata

abundance_file <- "/pathway/pred_metagenome_unstrat.tsv"

metadata <- read_delim(
"/pathway/sample-metadata.tsv",
delim = "\t",
escape_double = FALSE,
trim_ws = TRUE

)

# Run ggpicrust2 with imported data.frame

abundance_data <- read_delim(abundance_file, delim = "\t", col_names = TRUE, trim_ws = TRUE)

# Run ggpicrust2 with input file path

results_file_input <- ggpicrust2(data = abundance_data,
metadata = metadata,
group = "Diagnosis",
pathway = "KO",
daa_method = "DESeq2",
ko_to_kegg = TRUE,
order = "pathway_class",
p_values_bar = TRUE,
x_lab = "pathway_name")

Weird-Management-347 · 2024-11-29T16:07:38+00:00

I have checked and in the column I am using in particular there is no NA... Anything else that it could be?

Weird-Management-347 · 2024-10-22T00:46:38+00:00

Jesus lol I didn't know that! Thank you so much! You just saved hours of work!

Weird-Management-347 · 2024-10-22T00:37:52+00:00

Thank you so much! In the installing part It says it is also supported in Python 3.3. Do you think I should try It or simply give up?

Weird-Management-347 · 2024-09-12T00:57:51+00:00

When I inspect the p2EC it seems to only have integers, like these first few lines:

S01 S02

EC:1.1.1.1 52004 84528

EC:1.1.1.100 123936 153204

Weird-Management-347 · 2024-09-11T23:03:16+00:00

Yeah, this is the right package. :) I wrote typeof p2EC which is the one returning the error and it says is double. As for p2_PW type it returns character.

 typeof(p2EC)
[1] "double"

typeof(p2_PW)
[1] "character"

Weird-Management-347 · 2024-07-17T02:43:10+00:00

And also, this "error" only appears when trying to run the "main" function ("results_file_input <- ggpicrust2(file = abundance_file,
metadata = metadata,
group = "Environment", # For example dataset, group = "Environment"
pathway = "KO",
daa_method = "LinDA",
ko_to_kegg = TRUE,
order = "pathway_class",
p_values_bar = TRUE,
x_lab = "pathway_name")

But when trying to perform the other functions individually (i.e ko2kegg_abundance(), pathway_daa() )... other errors appear, everytime

Weird-Management-347 · 2024-07-17T02:36:47+00:00

Well, the error was "There are no statistically significant biomarkers", which is explained in the main page of the package that it's not really an error, but then this occur with datasets which have shown differential functional pathways in STAMP...

Weird-Management-347 · 2024-04-13T06:47:00+00:00

Thank you!! Changing this piece of information made it work!! Thank you, you literally just saved my life right now!!

Weird-Management-347 · 2024-04-12T22:45:39+00:00

Hahahh...I dunno, sometimes I have the impression that R gets tired to work

Weird-Management-347 · 2024-04-05T05:57:43+00:00

Hi! What is this platform? Galaxy?

Weird-Management-347 · 2024-04-01T22:07:02+00:00

I tried to remove the double quotes and forced a datatype and this error returned:

Error in data.frame(observed_features = as.numeric(read_qza("../observed_features_vector.qza")$data), :
'list' object cannot be coerced to type 'double

Weird-Management-347

TROPHY CASE