# \#R **URL:** https://help.c-moor.org/tag/r/40.md [Latest](https://help.c-moor.org/latest.md) · [Categories](https://help.c-moor.org/categories.md) · [Tags](https://help.c-moor.org/tags.md) --- ## [Creating 100% stacked bar charts with merge\_samples](https://help.c-moor.org/t/creating-100-stacked-bar-charts-with-merge-samples/565)
**Author:** [@syork](https://help.c-moor.org/u/syork)\ **Replies:** 0\ **Last updated:** [July 22, 2025, 1:26am UTC](https://help.c-moor.org/t/creating-100-stacked-bar-charts-with-merge-samples/565 "2025-07-22T01:26:04Z")
How to create a 100% stacked bar chart using data in phyloseq! There are some extra steps here because we are working with a categorical variable. It seems that when you use a continuous variable like age there may not … --- ## [Every gene contains at least one zero, cannot compute log geometric means](https://help.c-moor.org/t/every-gene-contains-at-least-one-zero-cannot-compute-log-geometric-means/560)
**Author:** [@syork](https://help.c-moor.org/u/syork)\ **Replies:** 5\ **Last updated:** [July 20, 2025, 7:22pm UTC](https://help.c-moor.org/t/every-gene-contains-at-least-one-zero-cannot-compute-log-geometric-means/560 "2025-07-20T19:22:08Z")
When running differential expression analysis, we see this error: my\_ad\_DESeq2 \<- phyloseq\_to\_deseq2(ad\_counts, design = ~group) my\_comparison \<- c("group", "AD", "control") Significant\_DEseq2\_ASVs \<- Differential\_Abund… --- ## [Indicator analysis](https://help.c-moor.org/t/indicator-analysis/561)
**Author:** [@syork](https://help.c-moor.org/u/syork)\ **Replies:** 0\ **Last updated:** [July 19, 2025, 6:09pm UTC](https://help.c-moor.org/t/indicator-analysis/561 "2025-07-19T18:09:11Z")
INDICATOR SPECIES ANALYSIS #Uses a sequence table from your phyloseq object What ASVs are exclusive to each group (ex. control vs disease state)? #Guides #Indicator Species Analysis in R #Indicator species analysis •… --- ## [Trouble with tax plots](https://help.c-moor.org/t/trouble-with-tax-plots/559)
**Author:** [@gugulethusk](https://help.c-moor.org/u/gugulethusk)\ **Replies:** 1\ **Last updated:** [July 17, 2025, 4:25pm UTC](https://help.c-moor.org/t/trouble-with-tax-plots/559 "2025-07-17T16:25:01Z")
I keep getting almost completely black bar plots when subsetting 16s data. Like this: @syork I’ve tried reloading and changing browsers, deleting and creating a new container, to no avail. Is there a problem with… --- ## [Need Coding Help](https://help.c-moor.org/t/need-coding-help/466)
**Author:** [@graceekalle](https://help.c-moor.org/u/graceekalle)\ **Replies:** 5\ **Last updated:** [March 6, 2025, 8:29pm UTC](https://help.c-moor.org/t/need-coding-help/466 "2025-03-06T20:29:59Z")
Hi! I am trying to work through a coding tutorial on R on a public restroom bacteria dataset. I’ll link it here: DIY: public restroom bacteria As I am importing my data ( The zipfile has been moved to a new location: h… --- ## [Unable to get any data Wnt1 or Wnt10b in R-Studio](https://help.c-moor.org/t/unable-to-get-any-data-wnt1-or-wnt10b-in-r-studio/311)
**Author:** [@Mark\_Sandwich](https://help.c-moor.org/u/Mark_Sandwich)\ **Replies:** 10\ **Last updated:** [July 21, 2022, 3:34pm UTC](https://help.c-moor.org/t/unable-to-get-any-data-wnt1-or-wnt10b-in-r-studio/311 "2022-07-21T15:34:52Z")
My R-Studio crashed and for some reason, I’m able to get most Wnt genes to plot their expression except for Wnt1 and Wnt10b, both of which are central to my poster. I brushed off the crash message thinking it was a regul… --- ## [Multiple Highest value points on top of UMAP](https://help.c-moor.org/t/multiple-highest-value-points-on-top-of-umap/305)
**Author:** [@Mark\_Sandwich](https://help.c-moor.org/u/Mark_Sandwich)\ **Replies:** 8\ **Last updated:** [July 20, 2022, 11:33pm UTC](https://help.c-moor.org/t/multiple-highest-value-points-on-top-of-umap/305 "2022-07-20T23:33:51Z")
Hi @mmccoy, I was able to graph out a Umap with the highest value points alongside the regular Umaps. I was only able to get one though because whenever I ran the code with two I got this message. I also got thes… --- ## [What embryonic stage/day is covered in the Mixed gastrulation and full data set we are provided through the R](https://help.c-moor.org/t/what-embryonic-stage-day-is-covered-in-the-mixed-gastrulation-and-full-data-set-we-are-provided-through-the-r/307)
**Author:** [@ShamounDivanyan](https://help.c-moor.org/u/ShamounDivanyan)\ **Replies:** 2\ **Last updated:** [July 19, 2022, 3:51pm UTC](https://help.c-moor.org/t/what-embryonic-stage-day-is-covered-in-the-mixed-gastrulation-and-full-data-set-we-are-provided-through-the-r/307 "2022-07-19T15:51:24Z")
What specific “time frame” are we given in the development of the mouse embryo? What I really need to know is what stages the data set is started on and cut off at? --- ## [Help on R code to identify specific cells expressing lefty1 or lefty2](https://help.c-moor.org/t/help-on-r-code-to-identify-specific-cells-expressing-lefty1-or-lefty2/274)
**Author:** [@yanethp](https://help.c-moor.org/u/yanethp)\ **Replies:** 1\ **Last updated:** [June 17, 2022, 3:01pm UTC](https://help.c-moor.org/t/help-on-r-code-to-identify-specific-cells-expressing-lefty1-or-lefty2/274 "2022-06-17T15:01:59Z")
@mmccoy @LindsayHayes @cpozmanter Last semester I analyzed the gene expression of Lefty1 and Lefty2. I focused on the differential expression of each within celltypes and found that they were both expressed in the defin… --- ## [Help - r4ds2 8-Putting it Together](https://help.c-moor.org/t/help-r4ds2-8-putting-it-together/207)
**Author:** [@Anastasia\_Khalilova](https://help.c-moor.org/u/Anastasia_Khalilova)\ **Replies:** 2\ **Last updated:** [March 2, 2022, 12:01am UTC](https://help.c-moor.org/t/help-r4ds2-8-putting-it-together/207 "2022-03-02T00:01:47Z")
I’ve been trying for about an hour or two on how to fix this error and I’m still lost as to what to do. It says that any of the variable I put in (eg “state” or “disease”) of the data set that it can’t find the object… --- ## [Help on Mouse gastrulation R Notebook](https://help.c-moor.org/t/help-on-mouse-gastrulation-r-notebook/189)
**Author:** [@yanethp](https://help.c-moor.org/u/yanethp)\ **Replies:** 2\ **Last updated:** [February 21, 2022, 6:48pm UTC](https://help.c-moor.org/t/help-on-mouse-gastrulation-r-notebook/189 "2022-02-21T18:48:06Z")
I’m having trouble with the third activity. Anything past chunk 2 won’t run, so when I try to run any chunk with metadata.df in it, it doesn’t work. --- ## ["host is down "](https://help.c-moor.org/t/host-is-down/86)
**Author:** [@tognibene](https://help.c-moor.org/u/tognibene)\ **Replies:** 3\ **Last updated:** [September 28, 2021, 7:17pm UTC](https://help.c-moor.org/t/host-is-down/86 "2021-09-28T19:17:56Z")
How do I resolve this when trying to load :test-driveR --- ## [503 Proxy Target Missing](https://help.c-moor.org/t/503-proxy-target-missing/73)
**Author:** [@madisonishigaki](https://help.c-moor.org/u/madisonishigaki)\ **Replies:** 2\ **Last updated:** [September 3, 2021, 5:09pm UTC](https://help.c-moor.org/t/503-proxy-target-missing/73 "2021-09-03T17:09:28Z")
When I try to go into the r4ds tutorials in the R Notebook, I get this error: --- ## [Missing retina.nb.html file](https://help.c-moor.org/t/missing-retina-nb-html-file/67)
**Author:** [@madisonishigaki](https://help.c-moor.org/u/madisonishigaki)\ **Replies:** 1\ **Last updated:** [August 27, 2021, 6:22pm UTC](https://help.c-moor.org/t/missing-retina-nb-html-file/67 "2021-08-27T18:22:42Z")
I followed the presentation on how to download the retina.Rmd files but I can’t locate the retina.nb.html file. Then when I try to export the retina.html, my computer opens a new tab and I get a 404 error. --- ## [Practice RStudio Console](https://help.c-moor.org/t/practice-rstudio-console/61)
**Author:** [@RosaAlcazar](https://help.c-moor.org/u/RosaAlcazar)\ **Replies:** 4\ **Last updated:** [August 24, 2021, 10:41pm UTC](https://help.c-moor.org/t/practice-rstudio-console/61 "2021-08-24T22:41:02Z")
Type any questions you have about the assignment! Did you get stuck? how did it go?