type分为了三个，代码对比了两个，出现了下面的问题

问题：

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Failed to create bus connection: No such file or directory

── Attaching core tidyverse packages ─────────────────────────────────────────────────────── tidyverse 2.0.0 ──

✔ dplyr     1.1.3     ✔ purrr     1.0.2

✔ forcats   1.0.0     ✔ stringr   1.5.0

✔ ggplot2   3.4.4     ✔ tidyr     1.3.0

✔ lubridate 1.9.3

── Conflicts ───────────────────────────────────────────────────────────────────────── tidyverse_conflicts() ──

✖ dplyr::filter() masks stats::filter()

✖ dplyr::lag()    masks stats::lag()

ℹ Use the conflicted package (<http://conflicted.r-lib.org/>) to force all conflicts to become errors

Warning message:

In system("timedatectl", intern = TRUE) :

  running command 'timedatectl' had status 1

Rows: 214 Columns: 5

── Column specification ───────────────────────────────────────────────────────────────────────────────────────

Delimiter: "\t"

chr (4): #SampleID, SampleName, group, type

dbl (1): Des

ℹ Use `spec()` to retrieve the full column specification for this data.

ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.

Error in data.frame(..., check.names = FALSE) :

  arguments imply differing number of rows: 173, 214

Calls: pathway_pca -> cbind -> cbind -> data.frame

Execution halted

附上代码

差异比较可视化

#其他差异比较：ALDEx2 , DESeq2, edgeR ,limma.voom,metagenomeSeq,LinDA,Maaslin2,Lefser

#代谢通路比较

for m in ALDEx2   DESeq2  edgeR limma.voom metagenomeSeq LinDA Maaslin2 Lefser;do

  Rscript $scriptdir/ggpicrust2.r --daa_method $m  \

    --pathway_table q2-picrust2_output/pathway_abundance.qza \

    -m $metadata -o q2-ggpicrust2_output \

    --top 20 --p_values_threshold 1 \

    -t type  -a  ACID -b DIA  -p pathway_type_q2

  # EC 酶 丰度比较

  Rscript $scriptdir/ggpicrust2.r --daa_method $m \

    --EC_table q2-picrust2_output/ec_metagenome.qza \

    -m $metadata -o q2-ggpicrust2_output \

    --top 20 --p_values_threshold 1 \

    -t type  -a  ACID -b DIA  -p EC_type_q2

  # KO 基因丰度比较

  Rscript $scriptdir/ggpicrust2.r --daa_method $m \

    --KO_table q2-picrust2_output/ko_metagenome.qza \

    -m $metadata -o q2-ggpicrust2_output \

    --top 20 --p_values_threshold 1 \

    -t type  -a  ACID -b DIA  -p KO_type_q2

done