guokai8 / microbial Goto Github PK

Hi Kai,

I need help in rearranging samples in the results of my taxonomy plot based on groups and relative abundance.

I used this script and produce this:

plotbar(norm,level="Phylum")

I want to reorder my samples like this:
sampleorder <- c(Control=c("YHY", "LJH", "KSH", "HSO", "LCH", "KHK", "HMG", "GYJ", "NYJ", "CYY"),(Patient=c("GSJ_R", "GSJ_L", "JSA_R", "OJY_L", "OJY_R", "CCS_L", "CCS_R", "PIR_R", "LEJ_L", "JSA_L", "LEJ_R", "KEJ_R", "KEJ_L", "PIR_L")))

Thanks
James

Hi Kai,

I get this error whenever I try these scripts in R:

ps
phyloseq-class experiment-level object
otu_table() OTU Table: [ 1052 taxa and 24 samples ]
sample_data() Sample Data: [ 24 samples by 2 sample variables ]
tax_table() Taxonomy Table: [ 1052 taxa by 8 taxonomic ranks ]

pp <- ldamarker(ps, pvalue = 0.05, normalize = TRUE, method = "relative")
Normalization using relative method
Error in $<-.data.frame(*tmp*, "tax", value = character(0)) :
replacement has 0 rows, data has 25248

May I ask some advice on how to resolve this.

Thanks
James

Thanks for providing this package.
I am trying to use it for plotting LDA.

The res table that I get from the function successfully, but when I use:

res <- ldamarker(ps_1,group="breastfeeding_group")
head(res,10)
# A tibble: 10 x 13
# Groups:   rank, tax [10]
   rank  tax      statistic p.value parameter method   p.adj `exclusive brea… `non-exclusive …   max
   <chr> <chr>        <dbl>   <dbl>     <int> <chr>    <dbl>            <dbl>            <dbl> <dbl>
 1 Class D_0__Ar…    1.00   0.316           1 Kruskal… 0.739              NA               NA    NA 
 2 Class D_0__Ba…    0.184  0.668           1 Kruskal… 0.872              NA               NA    NA 
 3 Class D_0__Ba…    1.13   0.288           1 Kruskal… 0.739              NA               NA    NA 
 4 Class D_0__Ba…    1.31   0.253           1 Kruskal… 0.739              NA               NA    NA 
 5 Class D_0__Ba…    0.0412 0.839           1 Kruskal… 0.955              NA               NA    NA 
 6 Class D_0__Ba…    2.28   0.131           1 Kruskal… 0.626              NA               NA    NA 
 7 Class D_0__Ba…    7.41   0.00649         1 Kruskal… 0.287             406.            1861. 1861.
 8 Class D_0__Ba…    3.83   0.0504          1 Kruskal… 0.510              NA               NA    NA 
 9 Class D_0__Ba…    0.169  0.681           1 Kruskal… 0.872              NA               NA    NA 
10 Class D_0__Ba…    0.144  0.704           1 Kruskal… 0.876              NA               NA    NA 
# … with 3 more variables: min <dbl>, LDAscore <dbl>, direction <chr>
plotLDA(res,group=c("exclusive breastfeeding","non-exclusive breastfeeding"),lda=5,pvalue=0.05)

The plot that generated is blank, only has a x-axis label.

Could you help me to address it ?
Thanks!

plotLDA(res,group=c("week_1","week_4", "week_24"),lda=2, pvalue=0.05)
Error: Insufficient values in manual scale. 3 needed but only 2 provided.

Is it possible to plot LDA for more than 2 groups?

Thanks

Hi! I wanted to know what these values are in the output table from ldamarker, I cant seem to find it anywhere in the documentation:
statistic, min and max.

Thank you!
Salma

I have sub-grouped the LDA plots by taxonomic level. However, I would only like to have the last rank name on the plot (e.g. phylum, genus etc) rather than the full string from Kingdom down.

I am struggling to manipulate the tax object to do this as it is a long string. Is there any chance there is an easy solution to this issue?

Thank you!
Susanne

Hi Kai

How do I cite the microbial package in the paper ?

Hesham

res <- ldamarker(ps.nonc.nocyano,group="SampleType")
Normalization using relative method
|========================================================================================================= |100% ~0 s remaining Error in $<-.data.frame(*tmp*, "direction", value = c("PFH", "SUH" :
replacement has 2 rows, data has 1
plotLDA(res,group=c("CFH","SUH"),lda=5,pvalue=0.05)
Error in subset(x, LDAscore > lda) : object 'res' not found