QIIME2R ->Error in UseMethod("left_join")

Sabrin · July 19, 2022, 2:20pm

Hi,
I am following this tutorial, GitHub - jbisanz/qiime2R: Import qiime2 artifacts to R, and have this error message when I reach alpha diversity step

Error in UseMethod("left_join") : **
** no applicable method for 'left_join' applied to an object of class "character"

yes most of my metadata file are chracters as when I was making it categorical I was getting another different error message unfortunately so instead of categorical I wrote character

Here is my metadata file

A_crassa.tsv (3.1 KB)

Thanks in advance for your help

jbisanz · July 19, 2022, 3:56pm

Could you post the particular code you are running when you hit this issue?

Sabrin · July 19, 2022, 3:57pm

metadata<-
metadata %>% 
  left_join(shannon)
head(metadata)

R output

metadata<-

metadata %>%
left_join(shannon)
Error in UseMethod("left_join") :
no applicable method for 'left_join' applied to an object of class "character"

head(metadata)

jbisanz · July 19, 2022, 4:31pm

You are sure you have a data.frame or tibble called shannon as opposed to a character vector? What happens if you look at class(shannon) or head(shannon)?

Sabrin · July 19, 2022, 4:42pm

> class(shannon)
[1] "list"
library(dplyr)    # alternatively, this also loads %>%

head(shannon) 
$uuid
[1] "43a6f70d-6910-415d-aa5e-1ca02bce7852"

$type
[1] "SampleData[AlphaDiversity]"

$format
[1] "AlphaDiversityDirectoryFormat"

$contents
                                                                                                            files.Name
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2                                                                         43a6f70d-6910-415d-aa5e-1ca02bce7852/VERSION
3                                                                   43a6f70d-6910-415d-aa5e-1ca02bce7852/checksums.md5
4                                                        43a6f70d-6910-415d-aa5e-1ca02bce7852/data/alpha-diversity.tsv
5                                                        43a6f70d-6910-415d-aa5e-1ca02bce7852/provenance/metadata.yaml
6                                                              43a6f70d-6910-415d-aa5e-1ca02bce7852/provenance/VERSION
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$version
          V1       V2
1      QIIME        2
2   archive:        5
3 framework: 2022.2.0

$data
       shannon_entropy
21Sed         8.318284
1Fg           3.627257
16Sg          7.214736
18Sg          8.294759
22Sed         8.216674
11Mg          7.324532
26SeaW        3.841162
20Sed         8.130349
14Mg          6.951016
2Mg           5.556254
25SeaW        3.357751
19Sg          7.907720
23Sed         8.447286
5Mg           6.886908
3Hg           7.206186
6Hg           7.351017
library(dplyr)    # alternatively, this also loads %>%

jbisanz · July 19, 2022, 4:56pm

Right, so that is not a table-like object. I think you missed this line in the tutorial:

shannon<-shannon$data %>% rownames_to_column("SampleID") # this moves the sample names to a new column that matches the metadata and allows them to be merged

Sabrin · July 20, 2022, 3:08pm

Thanks it works somehow now.

rigth now i am running

metadata %>%
filter(!is.na(shannon)) %>%
ggplot(aes(x=SampleID, y=shannon, color=Sample_type)) +
stat_summary(geom="errorbar", fun.data=mean_se, width=0) +
stat_summary(geom="line", fun.data=mean_se) +
stat_summary(geom="point", fun.data=mean_se) +
xlab("Samples") +
ylab("Shannon Diversity") +
theme_q2r() + # try other themes like theme_bw() or theme_classic()
scale_color_viridis_d(name="Sample_type") # use different color scale which is color blind friendly
ggsave("Shannon_by_Sample_type.pdf", height=3, width=4, device="pdf") # save a PDF 3 inches by 4 inches

but unfortunately getting this error message

rlang::last_error()
<error/rlang_error>
Error in filter():
! Problem while computing ..1 = !is.na(shannon).
Input ..1 must be a logical vector, not a logical[,2].

Backtrace:

metadata %>% filter(!is.na(shannon)) %>% ...
dplyr:::filter.data.frame(., !is.na(shannon))
Run rlang::last_trace() to see the full context.

Sorry, I am an R beginner

system · September 2, 2022, 1:16am

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