cafferychen777/ggpicrust2 issues and pull requests

#132 - The link provided in your paper regarding the shiny app is not working

Issue - State: closed - Opened by marwa38 22 days ago - 1 comment
Labels: bug

#131 - Question_Are_there_ways_to_combine_predicted_pathways_with_the_bacterial_genera_for_visualization?

Issue - State: open - Opened by ShevchenkoAlla about 2 months ago - 4 comments
Labels: bug

#130 - Error in value[[3L]](cond) : DESeq2 analysis failed: every gene contains at least one zero, cannot compute log geometric means

Issue - State: open - Opened by Liviacmg about 2 months ago - 2 comments
Labels: bug

#129 - Creating pathway error bar plots... Error in `$<-.data.frame`(`tmp`, "group", value = c(2L, 1L, 2L, 2L, : replacement has 179 rows, data has 1 In addition: Warning message: In cbind(sample = colnames(sub_relative_abundance_mat), group = Group, : number of rows of result is not a multiple of vector length (arg 2)

Issue - State: open - Opened by Liviacmg 2 months ago - 3 comments
Labels: bug

#128 - Is there a way to correlate KEGG pathways to taxa?

Issue - State: open - Opened by Liviacmg 2 months ago - 1 comment
Labels: bug

#127 - Using the test dataset: Error in x[, ii] : subscript out of bounds.

Issue - State: open - Opened by Lacona 2 months ago - 2 comments
Labels: bug

#126 - ko2kegg_abundance leads to 0 keggs

Issue - State: open - Opened by ranfoxall 2 months ago - 4 comments

#125 - Option to Display a Representative Sample Instead of All Replicates in the Plot

Issue - State: open - Opened by Niyuh04 2 months ago

#124 - Input file problem

Issue - State: open - Opened by ShevchenkoAlla 2 months ago - 7 comments
Labels: question

#123 - Choosing of selective metacyc pathway"ggpicrust2"

Issue - State: open - Opened by kesava31 3 months ago - 1 comment
Labels: bug

#122 - All my pathway results are NA

Issue - State: open - Opened by weiGu-88 3 months ago - 2 comments
Labels: bug

#121 - daa_method ="Maaslin2", is there more options adjusting models and other parameters other than the default setting?

Issue - State: open - Opened by shuqili 4 months ago - 1 comment

#120 - Question: how to gain annotation from KEGG IDs?

Issue - State: open - Opened by AMosca96 4 months ago - 1 comment
Labels: bug

#118 - pathway_heatmap can't extract columns past the end

Issue - State: open - Opened by luigallucci 5 months ago - 7 comments
Labels: bug

#117 - pathway_errorbar error

Issue - State: open - Opened by DeniRibicic 5 months ago - 7 comments
Labels: bug

#116 - # Perform pathway DAA using ALDEx2 method not working with example dataset

Issue - State: open - Opened by JayalalKJ 5 months ago - 1 comment
Labels: bug

#115 - pathway_annotation error "An error occurred. Retrying......"

Issue - State: open - Opened by jw0531jung 5 months ago - 4 comments
Labels: bug

#112 - Error in switch(file_format, .txt = abundance <- readr::read_delim(file, : EXPR must be a length 1 vector**

Issue - State: open - Opened by bplet01 6 months ago - 2 comments

#111 - Error pathway_errorbar "`$<-.data.frame`(`tmp`, "group", value = c(2L, 2L, 2L, 2L, : replacement has 20 rows, data has 1"

Issue - State: open - Opened by raqxavier 7 months ago - 4 comments
Labels: bug

#110 - Is this package compatible with other ggplot functions?

Issue - State: open - Opened by chung-wingko 8 months ago - 1 comment
Labels: bug

#109 - pathway_errorbar no longer working to graph data

Issue - State: open - Opened by AbbiHern 8 months ago - 1 comment
Labels: bug

#108 - pathway_pca

Issue - State: open - Opened by raqxavier 8 months ago - 4 comments

#107 - Help needed using sample dada Math.factor ‘round’ not meaningful for factors

Issue - State: open - Opened by jrhaulung 8 months ago - 2 comments
Labels: bug

#106 - All my pathway results are NA

Issue - State: open - Opened by Elixir0822 10 months ago - 1 comment
Labels: bug

#105 - The 'method' column in the 'daa_results_df' data frame contains more than one method.

Issue - State: open - Opened by freemutation 10 months ago - 5 comments
Labels: bug

#104 - curl_fetch_memory

Issue - State: open - Opened by mccannpeter 11 months ago - 4 comments
Labels: bug

#103 - How to obtain log-fold change values?

Issue - State: closed - Opened by andrewd789 11 months ago - 3 comments

#102 - undefined columns selected and ‘round’ not meaningful for factors

Issue - State: open - Opened by antonkratz 11 months ago - 4 comments
Labels: bug

#101 - Error in `guide_transform()`: ! <Guide> classes have been rewritten as <ggproto> classes.

Issue - State: open - Opened by antonkratz 11 months ago - 3 comments
Labels: bug

#100 - error with MicrobiomeStat

Issue - State: open - Opened by saassli21 11 months ago - 5 comments

#98 - Error in `plot_theme()`: ! The `legend.text.align` theme element is not defined in the element hierarchy.

Issue - State: closed - Opened by lananh-ngn 11 months ago - 2 comments
Labels: bug

#96 - Error in ggpicrust2 (There are no statistically significant biomarkers in the dataset)

Issue - State: open - Opened by erda712 11 months ago - 4 comments

#94 - Issue with pathway_errorbar : "The `legend.text.align` theme element is not defined in the element hierarchy."

Issue - State: closed - Opened by scilexenko 11 months ago - 6 comments
Labels: bug

#93 - Installation issues with Rfast

Issue - State: open - Opened by camcecc 12 months ago - 2 comments
Labels: bug

#92 - add a title to errorbar and heatmap

Issue - State: open - Opened by SueFletcher 12 months ago - 9 comments

#91 - Error from pathway_errorbar

Issue - State: open - Opened by lingvv 12 months ago - 1 comment

#90 - pathway_heatmap cannot reorder

Issue - State: open - Opened by gaimingle10 12 months ago - 1 comment
Labels: bug

#89 - pathway_daa()

Issue - State: open - Opened by manijehmahdavi about 1 year ago - 1 comment
Labels: bug

#88 - Question about filtering features and groups

Issue - State: open - Opened by pig-raffles about 1 year ago - 7 comments

#86 - pathway_errorbar() : The 'method' column in the 'daa_results_df' data frame contains more than one method. Please filter it to contain only one method.

Issue - State: open - Opened by IloveUKarna about 1 year ago - 3 comments
Labels: bug

#85 - Add website to DESCRIPTION

Pull Request - State: closed - Opened by olivroy about 1 year ago

#84 - Issue plotting LinDA results as heatmap when ko_to_kegg = FALSE

Issue - State: closed - Opened by BiggusDickus666 about 1 year ago - 4 comments

#82 - How to model for mixed effects?

Issue - State: open - Opened by otaviolovison about 1 year ago - 1 comment

#81 - ggpicrust on ITS : Error in `$<-.data.frame`(`tmp`, "description", value = character(0)) : le tableau de remplacement a 0 lignes, le tableau remplacé en a 1

Issue - State: open - Opened by SueFletcher about 1 year ago - 5 comments

#80 - Using ggpicrust2 for more than 2 groups.

Issue - State: closed - Opened by lcamVz about 1 year ago - 1 comment

#79 - Stratified data

Issue - State: open - Opened by BiggusDickus666 about 1 year ago - 2 comments

#78 - Error in if (dispersion == 1) "LRT" else "scaled dev." : missing value where TRUE/FALSE needed

Issue - State: open - Opened by Selucote8223 about 1 year ago - 6 comments

#76 - PICRUSt2 tsv file is unformatted/not recognized when opened in ggpicrust2

Issue - State: open - Opened by PaulaEterovick about 1 year ago - 2 comments

#75 - "Error in dim[2] - index pathway_heatmap

Issue - State: open - Opened by xinguo1236 about 1 year ago - 1 comment

#74 - pathway_errorbar nonspecific error

Issue - State: open - Opened by AbbiHern about 1 year ago - 9 comments

#72 - The 'group1' or 'group2' column in the 'daa_results_df' data frame contains more than one group. Please filter each to contain only one group.

Issue - State: open - Opened by saassli21 about 1 year ago - 6 comments

#71 - Issue with MetaCyc pathway annotation

Issue - State: open - Opened by etodd8 about 1 year ago

#70 - Question about p-value(adjusted) in errorbar graph

Issue - State: open - Opened by microbialkim about 1 year ago - 3 comments

#69 - errobar interpretation

Issue - State: open - Opened by saassli21 about 1 year ago - 5 comments

#68 - 'pathway_daa' function - Undefined colums selects

Issue - State: open - Opened by gonzalofe about 1 year ago - 3 comments

#67 - ALDex2 issue

Issue - State: open - Opened by SRuwi about 1 year ago - 9 comments

#66 - How to use plotly to generate interactive ggpicrust2 plots

Issue - State: open - Opened by ScarlettPegany over 1 year ago - 8 comments

#65 - issue while running pathway_errorbar()

Issue - State: open - Opened by DaliBAmor over 1 year ago - 20 comments

#64 - ggpicrust2(): Error in `metadata[, matching_columns]`:

Issue - State: open - Opened by WillErickson1 over 1 year ago - 10 comments

#63 - pathway_errorbar(): Editing the images generated using pathway error bar plot analysis

Issue - State: open - Opened by Aristotle1992 over 1 year ago - 12 comments

#62 - ggpicrust2(): incorrect number of dimensions

Issue - State: open - Opened by luomeng277 over 1 year ago - 1 comment

#60 - ggpicrust2 input file

Issue - State: closed - Opened by DaliBAmor over 1 year ago - 3 comments

#58 - pathway_daa(): Error in metadata[, matching_columns]: ! Can't subset columns with matching_columns. ✖ Subscript matching_columns can't contain missing values. ✖ It has a missing value at location 1.

Issue - State: open - Opened by GeoffreyOlweny over 1 year ago - 6 comments

#57 - pathway_errorbar(): In the results of the pathway_errorbar plot, the p-values cannot be fully displayed

Issue - State: closed - Opened by benzodiazepines over 1 year ago - 1 comment

#56 - pathway_daa(): Error in Math.factor(c(1L, 1L, 1L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 2L, 1L, : ‘round’ not meaningful for factors

Issue - State: closed - Opened by nicharee22 over 1 year ago - 5 comments

#55 - ggpicrust Install Issues

Issue - State: closed - Opened by ZellaD over 1 year ago - 2 comments

#54 - docs: add otaviolovison as a contributor for code

Pull Request - State: closed - Opened by allcontributors[bot] over 1 year ago

#53 - Bot test

Issue - State: closed - Opened by cafferychen777 over 1 year ago - 2 comments

#52 - @all-contributors please init

Issue - State: closed - Opened by cafferychen777 over 1 year ago

#51 - compare_daa_results(): Maaslin2 method changed the names of the metacyc pathways, replacing a hyphen (-) with a dot (.)

Issue - State: closed - Opened by dgkurt over 1 year ago - 5 comments
Labels: enhancement

#50 - pathway_errorbar(): "The 'group1' or 'group2' column in the 'daa_results_df' data frame contains more than one group. Please filter each to contain only one group."

Issue - State: closed - Opened by otaviolovison over 1 year ago - 8 comments
Labels: enhancement

#49 - pathway_errorbar(): color was not mapped on the road when saving

Issue - State: closed - Opened by kestlermai over 1 year ago - 4 comments

#48 - Error: could not find function "memory.limit" Execution halted Warning in install.packages : installation of package 'ggpicrust2' had non-zero exit status

Issue - State: open - Opened by XingChengguang over 1 year ago - 1 comment

#47 - Question: how to extract mapping data in `pathway_errorbar`

Issue - State: closed - Opened by Rainjie-afk over 1 year ago - 2 comments

#45 - My pred_metagenome_unstrat file has EC:1.1.1.1 and not KO format

Issue - State: closed - Opened by Aristotle1992 over 1 year ago - 8 comments

#44 - pathway_errorbar(): Error: Index out of bounds

Issue - State: closed - Opened by UrielEspinoza over 1 year ago - 11 comments

#42 - pathway_errorbar(): Can't add `e2` to a <ggplot> object.

Issue - State: closed - Opened by Aristotle1992 over 1 year ago - 3 comments
Labels: documentation

#40 - pathway_daa(): object 'p_values_df' not found"

Issue - State: closed - Opened by carmennns2 over 1 year ago - 15 comments
Labels: good first issue

#39 - Error in pathway_errorbar(abundance = metcyc_abundance_data %>% column_to_rownames("pathway"), : The feature with statistically significance is zero, pathway_errorbar can't do the visualization.

Issue - State: closed - Opened by mayagabitzsch over 1 year ago - 1 comment
Labels: duplicate

#38 - pathway_pca(): Error in prcomp.default(t(abundance), center = TRUE, scale = TRUE) : cannot rescale a constant/zero column to unit variance

Issue - State: closed - Opened by mayagabitzsch over 1 year ago - 3 comments
Labels: invalid

#37 - ggpicrust2 installation dependency error

Issue - State: open - Opened by xuan13hao over 1 year ago - 4 comments
Labels: invalid

#36 - Update README.md

Pull Request - State: closed - Opened by cafferychen777 over 1 year ago

#35 - pathway_daa(): Error in metadata[, matching_columns]: ! Can't subset columns with matching_columns. ✖ Subscript matching_columnscan't contain missing values. ✖ It has a missing value at location 1. Runrlang::last_trace()

Issue - State: closed - Opened by mayagabitzsch over 1 year ago - 7 comments
Labels: invalid

#34 - pathway_errorbar(): `levels<-`(`tmp`, value = as.character(levels)) : factor level [3] is duplicated

Issue - State: closed - Opened by Lacona over 1 year ago - 12 comments

#33 - ko2kegg_abundance(): KO2Kegg abundance returning empty output.

Issue - State: closed - Opened by lcamVz over 1 year ago - 3 comments
Labels: good first issue

#32 - finding KO's that contributed to KEGG pathway, KO_to_kegg=FALSE, and Implementing LEfSe

Issue - State: closed - Opened by kriegerm over 1 year ago - 4 comments
Labels: documentation

#30 - "FuncDiv" for functional diversity visualization using ggpicrust2?

Issue - State: closed - Opened by marwa38 over 1 year ago - 7 comments
Labels: enhancement

#29 - What is the statistical test applied by metagenomeSeq?

Issue - State: closed - Opened by Teo2091 over 1 year ago - 3 comments
Labels: documentation

#28 - Questions about KEGG pathways

Issue - State: open - Opened by andressamv over 1 year ago - 1 comment
Labels: good first issue

#27 - Question: how to annotate pathway information using the output file from PICRUSt2?

Issue - State: closed - Opened by LiaOb21 over 1 year ago - 15 comments

#26 - pathway_daa(): Error in contrasts<-(tmp, value = contr.funs[1 + isOF[nn]]) : contrasts can be applied only to factors with 2 or more levels

Issue - State: open - Opened by andressamv over 1 year ago - 6 comments
Labels: wontfix

#25 - Error after pathway_errorbar

Issue - State: closed - Opened by andressamv over 1 year ago - 19 comments

#24 - ggpicrust2(): Error in .rowNamesDF<-(x, value = value) : invalid 'row.names' length

Issue - State: closed - Opened by mbrose2022 over 1 year ago - 13 comments
Labels: invalid

#23 - pathway_daa(): There are no statistically significant biomarkers

Issue - State: open - Opened by GeoffreyOlweny over 1 year ago - 4 comments
Labels: duplicate

#22 - pathway_annotation(): Error in $<-.data.frame(tmp, "pathway_description"

Issue - State: closed - Opened by kaw97 almost 2 years ago - 9 comments

#21 - pathway_heatmap not returning as expected

Issue - State: closed - Opened by hharder1 almost 2 years ago - 13 comments
Labels: enhancement

#20 - pathway_errorbar(): "Error in guide_train.prism_offset_minor" when ggprism loaded

Issue - State: closed - Opened by erikpark almost 2 years ago - 3 comments

#19 - pathway_annotation() long runtime, connecting to KEGG database

Issue - State: open - Opened by erikpark almost 2 years ago - 6 comments
Labels: duplicate

#18 - pathway_errorbar(): Error: Index out of bounds

Issue - State: closed - Opened by RayKramp1 almost 2 years ago - 4 comments

#17 - pathway_annotation issue

Issue - State: closed - Opened by KitHubb almost 2 years ago - 5 comments

GitHub / cafferychen777/ggpicrust2 issues and pull requests