Color bar not showing up for term_enrichment_graph

Hello,

UPDATE: I meant term_gene_heatmap() like in the code. Looking at too many codes. Sorry for the confusion.

I am running the same data sets though UpSet_plot() and term_enrichment_graph () but I am only getting the legend for UpSet_Plot() - please see pictures. When I run term_enrichment_graph() I get the following warning:

> term<-term_gene_heatmap(cluster_glut1[cluster_glut1$Status=="Representative",], glut1_combo, use_description = TRUE, low = 'purple', high = 'yellow', num_terms = 20, pin_name_path = "mmu_STRING") Number of genes provided in input: 100 Number of genes in input after p-value filtering: 100 pathfindR cannot handle p values < 1e-13. These were changed to 1e-13 Could not find any interactions for 28 (28%) genes in the PIN Final number of genes in input: 72 Warning message: guides( = FALSE)is deprecated. Please useguides( = "none")instead.

For comparison, here is what I am using for the UpSet_plot command: UpSet_plot(cluster_glut1[cluster_glut1$Status=="Representative",], glut1_combo, use_description = TRUE, low = 'purple', high = 'yellow', num_terms = 20, pin_name_path = "mmu_STRING")

My searching for someone with a similar problem in ggvenn revealed that there was something about how specific programs are interacting with ggplot2 after recent updates. Is there another term I should now be adding to term_enrichment_graph()?

Thanks again for the great program, Ana

R version 4.0.5 (2021-03-31) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Red Hat Enterprise Linux 8.2 (Ootpa)

Matrix products: default BLAS: /cm/shared/apps_chop/R/4.0.5/lib64/R/lib/libRblas.so LAPACK: /cm/shared/apps_chop/R/4.0.5/lib64/R/lib/libRlapack.so

locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8
[4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages: [1] stats graphics grDevices utils datasets methods base

other attached packages: [1] forcats_0.5.1 stringr_1.4.0 dplyr_1.0.7 purrr_0.3.4
[5] readr_2.0.0 tidyr_1.1.3 tibble_3.1.3 ggplot2_3.3.5
[9] tidyverse_1.3.1 pathfindR_1.6.1 pathfindR.data_1.1.1 readxl_1.3.1

loaded via [1] fs_1.5.0 [5] doParallel_1.0.16 [9] bslib_0.2.5.1 [13] BiocGenerics_0.36.1 [17] tidyselect_1.1.1 [21] rvest_1.0.1 [25] labeling_0.4.2 [29] DEoptimR_1.0-9 [33] rmarkdown_2.10 [37] dbplyr_2.1.1 [41] rstudioapi_0.13 [45] generics_0.1.0 [49] magrittr_2.0.1 [53] S4Vectors_0.28.1 [57] R.methodsS3_1.8.1 [61] MASS_7.3-53.1 [65] blob_1.2.2 [69] lattice_0.20-41 [73] magick_2.7.2 [77] fpc_2.2-9 [81] glue_1.4.2 [85] vctrs_0.3.8 [89] gtable_0.3.0 [93] cachem_1.0.5 [97] tidygraph_1.2.0 [101] tinytex_0.33 [105] cluster_2.1.1 a namespace (and not attached): lubridate_1.7.10 bit64_4.0.5 httr_1.4.2
prabclus_2.3-2 backports_1.2.1 tools_4.0.5
utf8_1.2.2 R6_2.5.0 DBI_1.1.1
colorspace_2.0-2 nnet_7.3-15 withr_2.4.2
gridExtra_2.3 bit_4.0.4 compiler_4.0.5
cli_3.0.1 Biobase_2.50.0 xml2_1.3.2
sass_0.4.0 diptest_0.76-0 scales_1.1.1
robustbase_0.93-8 digest_0.6.27 ggupset_0.3.0
R.utils_2.10.1 pkgconfig_2.0.3 htmltools_0.5.1.1
fastmap_1.1.0 highr_0.9 rlang_0.4.11
RSQLite_2.2.7 jquerylib_0.1.4 farver_2.1.0
jsonlite_1.7.2 mclust_5.4.7 R.oo_1.24.0
modeltools_0.2-23 Rcpp_1.0.7 munsell_0.5.0
fansi_0.5.0 viridis_0.6.1 lifecycle_1.0.0
stringi_1.7.3 yaml_2.2.1 ggraph_2.0.5
flexmix_2.3-17 org.Hs.eg.db_3.12.0 grid_4.0.5
parallel_4.0.5 ggrepel_0.9.1 crayon_1.4.1
haven_2.4.3 graphlayouts_0.7.1 hms_1.1.0
knitr_1.33 pillar_1.6.2 igraph_1.2.6
codetools_0.2-18 stats4_4.0.5 reprex_2.0.1
evaluate_0.14 modelr_0.1.8 tzdb_0.1.2
tweenr_1.0.2 foreach_1.5.1 cellranger_1.1.0
polyclip_1.10-0 kernlab_0.9-29 assertthat_0.2.1
xfun_0.25 ggforce_0.3.3 broom_0.7.9
class_7.3-18 viridisLite_0.4.0 iterators_1.0.13
AnnotationDbi_1.52.0 memoise_2.0.0 IRanges_2.24.1
ellipsis_0.3.2

UpSet_glut1 term_heatmap_glut1

egeulgen / pathfindR

Color bar not showing up for term_enrichment_graph #95