browaeysrobin
commented
7 months ago Hi @Isabellvse
Now you wrote:
contrasts_oi = c("'A-B', 'C-B'")
Whereas the original code only works with this:
contrasts_oi = c("'A-B','C-B'")
so without the space behind the comma
Therefore you had to adapt the code to remove the " " as well (but not really a problem if you do it this way).
Hello,
I am following this tutorial:
https://github.com/saeyslab/multinichenetr/blob/main/vignettes/threewise_analysis_MISC.md
But I get an error when I run the following function in step 2:
(Note: I have not made any changes to this)
multinichenet_output = multi_nichenet_analysis(sce = sce, celltype_id = celltype_id, sample_id = sample_id, group_id = group_id, lr_network = lr_network, ligand_target_matrix = ligand_target_matrix, contrasts_oi = contrasts_oi, contrast_tbl = contrast_tbl, batches = batches, covariates = covariates, prioritizing_weights = prioritizing_weights, min_cells = min_cells, logFC_threshold = logFC_threshold, p_val_threshold = p_val_threshold, fraction_cutoff = fraction_cutoff, p_val_adj = p_val_adj, empirical_pval = empirical_pval, top_n_target = top_n_target, n.cores = n.cores, sender_receiver_separate = FALSE, verbose = TRUE)I got the following error:
Error in multi_nichenet_analysis_combined(...) : conditions written in contrasts_oi should be in the contrast column of contrast_tbl column! This is not the case, which can lead to errors downstream.
I looked in the code for multi_nichenet_analysis_combined, and the error occurs when creating the contrasts_oi_simplified
contrasts_oi_simplified = stringr::str_split(contrasts_oi, "'") %>% unlist() %>% unique() %>% stringr::str_split(",") %>% unlist() %>% unique() %>% generics::setdiff(c("", ",")) %>% unlist() %>% unique()This creates a vector that looks like this:
"A-B" " " "C-B", the " " is not removed.I added this to the
generics::setdiff(c("", ","))so it becomesgenerics::setdiff(c("", ",", " "))The full code:
contrasts_oi_simplified = stringr::str_split(contrasts_oi, "'") %>% unlist() %>% unique() %>% stringr::str_split(",") %>% unlist() %>% unique() %>% generics::setdiff(c("", ",", " ")) %>% unlist() %>% unique()and this creates a vector that looks like this:
"A-B" "C-B"And I am now able to run the command.
This is how I created the contrasts_oi and contrast_tbl
`contrasts_oi = c("'A-B', 'C-B'")
contrast_tbl = tibble(contrast = c('A-B', 'C-B'), group = c("A", "C")) ` Is there something I am doing wrong when creating the contrast_oi and contrast_tbl?
Kind Regards, Isabell
Session info:
`R version 4.3.0 (2023-04-21) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 22.04.1 LTS
Matrix products: default BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.10.0 LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0
locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8
[6] LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
time zone: Europe/Berlin tzcode source: system (glibc)
attached base packages: [1] stats4 stats graphics grDevices utils datasets methods base
other attached packages: [1] SingleCellExperiment_1.24.0 SummarizedExperiment_1.32.0 Biobase_2.62.0 GenomicRanges_1.54.1 GenomeInfoDb_1.38.1
[6] IRanges_2.36.0 S4Vectors_0.40.2 BiocGenerics_0.48.1 MatrixGenerics_1.14.0 matrixStats_1.2.0
[11] ggplot2_3.4.4 dplyr_1.1.4 Signac_1.12.0 SeuratObject_5.0.1 Seurat_4.4.0
[16] multinichenetr_1.0.3
loaded via a namespace (and not attached): [1] progress_1.2.3 nnet_7.3-18 locfdr_1.1-8 goftest_1.2-3 Biostrings_2.70.1
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[16] MASS_7.3-58.4 reshape2_1.4.4 httpuv_1.6.13 foreach_1.5.2 withr_2.5.2
[21] xfun_0.41 ggpubr_0.6.0 ellipsis_0.3.2 survival_3.5-5 memoise_2.0.1
[26] ggbeeswarm_0.7.2 emmeans_1.8.9 zoo_1.8-12 GlobalOptions_0.1.2 gtools_3.9.5
[31] pbapply_1.7-2 Formula_1.2-5 prettyunits_1.2.0 KEGGREST_1.42.0 promises_1.2.1
[36] httr_1.4.7 rstatix_0.7.2 globals_0.16.2 fitdistrplus_1.1-11 rstudioapi_0.14
[41] miniUI_0.1.1.1 generics_0.1.3 base64enc_0.1-3 zlibbioc_1.48.0 ScaledMatrix_1.10.0
[46] ggraph_2.1.0 polyclip_1.10-6 randomForest_4.7-1.1 GenomeInfoDbData_1.2.11 SparseArray_1.2.2
[51] xtable_1.8-4 stringr_1.5.1 doParallel_1.0.17 evaluate_0.23 S4Arrays_1.2.0
[56] hms_1.1.3 irlba_2.3.5.1 colorspace_2.1-0 visNetwork_2.1.2 ROCR_1.0-11
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[121] checkmate_2.3.1 DelayedMatrixStats_1.24.0 Rdpack_2.6 ggsignif_0.6.4 estimability_1.4.1
[126] tibble_3.2.1 Matrix_1.6-4 statmod_1.5.0 tzdb_0.4.0 fANCOVA_0.6-1
[131] tweenr_2.0.2 pkgconfig_2.0.3 tools_4.3.0 cachem_1.0.8 RSQLite_2.3.4
[136] RhpcBLASctl_0.23-42 rbibutils_2.2.16 DBI_1.1.3 viridisLite_0.4.2 numDeriv_2016.8-1.1
[141] fastmap_1.1.1 rmarkdown_2.25 scales_1.3.0 grid_4.3.0 ica_1.0-3
[146] Rsamtools_2.16.0 nichenetr_2.0.4 broom_1.0.5 patchwork_1.1.3 coda_0.19-4
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[166] uwot_0.1.16 glmmTMB_1.1.8 mvtnorm_1.2-4 bluster_1.12.0 lava_1.7.3
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[176] rjson_0.2.21 ggridges_0.5.4 progressr_0.14.0 parallel_4.3.0 pROC_1.18.5
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[196] htmltools_0.5.7 sctransform_0.4.1 glue_1.6.2 factoextra_1.0.7 spam_2.10-0
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[211] R6_2.5.1 sva_3.50.0 tidyr_1.3.0 DESeq2_1.42.0 gplots_3.1.3
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[236] RColorBrewer_1.1-3 rlang_1.1.2 spatstat.sparse_3.0-3 spatstat.explore_3.2-5 lmerTest_3.1-3
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