Comments (13)
guokai8
commented on June 3, 2024
Hi @Hesham999666 ,
Could you provide the detail for you group information for your sample?
Kai
from microbial.
Hesham999666
commented on June 3, 2024
Hi Kai
print (ps.nonc.nocyano)
phyloseq-class experiment-level object
otu_table() OTU Table: [ 37104 taxa and 357 samples ]
sample_data() Sample Data: [ 357 samples by 2 sample variables ]
tax_table() Taxonomy Table: [ 37104 taxa by 6 taxonomic ranks ]
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guokai8
commented on June 3, 2024
Please use
head(phyloseq::sample_data(ps.nonc.nocyano))
to show the information
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Hesham999666
commented on June 3, 2024
Sample Data: [6 samples by 2 sample variables]:
SampleType Sample2
1001SH CFH 1001SH
1001WH CFH 1001WH
1001WS CS 1001WS
1009SH CFH 1009SH
1009WH CFH 1009WH
1009WS CS 1009WS
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guokai8
commented on June 3, 2024
Do you have the same sample name (1001SH ...) as the colnames for the count_table?
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Hesham999666
commented on June 3, 2024
No it is empty , it did not show when I run head (phyloseq::sample_data(ps.nonc.nocyano))
but this from metadata file
Sample,SampleType,Sample2
1001SH,CFH,1001SH
1001WH,CFH,1001WH
that is why I add third column (kind of bug)
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guokai8
commented on June 3, 2024
which one is empty?
And Please check the format if it looks same as my example data:
> data(Physeq)
> physeq
phyloseq-class experiment-level object
otu_table() OTU Table: [ 19216 taxa and 26 samples ]
sample_data() Sample Data: [ 26 samples by 8 sample variables ]
tax_table() Taxonomy Table: [ 19216 taxa by 7 taxonomic ranks ]
phy_tree() Phylogenetic Tree: [ 19216 tips and 19215 internal nodes ]
> head(otu_table(physeq))
OTU Table: [6 taxa and 26 samples]
taxa are rows
CL3 CC1 SV1 M31Fcsw M11Fcsw M31Plmr M11Plmr F21Plmr M31Tong M11Tong
549322 0 0 0 0 0 0 0 0 0 0
522457 0 0 0 0 0 0 0 0 0 0
951 0 0 0 0 0 0 1 0 0 0
244423 0 0 0 0 0 0 0 0 0 0
586076 0 0 0 0 0 0 0 0 0 0
246140 0 0 0 0 0 0 0 0 0 0
LMEpi24M SLEpi20M AQC1cm AQC4cm AQC7cm NP2 NP3 NP5 TRRsed1 TRRsed2
549322 0 1 27 100 130 1 0 0 0 0
522457 0 0 0 2 6 0 0 0 0 0
951 0 0 0 0 0 0 0 0 0 0
244423 0 0 0 22 29 0 0 0 0 0
586076 0 0 0 2 1 0 0 0 0 0
246140 0 0 0 1 3 0 0 0 0 0
TRRsed3 TS28 TS29 Even1 Even2 Even3
549322 0 0 0 0 0 0
522457 0 0 0 0 0 0
951 0 0 0 0 0 0
244423 0 0 0 0 0 0
586076 0 0 0 0 0 0
246140 0 0 0 0 0 0
> head(sample_data(physeq))
Sample Data: [6 samples by 8 sample variables]:
X.SampleID Primer Final_Barcode Barcode_truncated_plus_T
CL3 CL3 ILBC_01 AACGCA TGCGTT
CC1 CC1 ILBC_02 AACTCG CGAGTT
SV1 SV1 ILBC_03 AACTGT ACAGTT
M31Fcsw M31Fcsw ILBC_04 AAGAGA TCTCTT
M11Fcsw M11Fcsw ILBC_05 AAGCTG CAGCTT
M31Plmr M31Plmr ILBC_07 AATCGT ACGATT
Barcode_full_length SampleType
CL3 CTAGCGTGCGT Soil
CC1 CATCGACGAGT Soil
SV1 GTACGCACAGT Soil
M31Fcsw TCGACATCTCT Feces
M11Fcsw CGACTGCAGCT Feces
M31Plmr CGAGTCACGAT Skin
Description group
CL3 Calhoun South Carolina Pine soil, pH 4.9 B
CC1 Cedar Creek Minnesota, grassland, pH 6.1 B
SV1 Sevilleta new Mexico, desert scrub, pH 8.3 B
M31Fcsw M3, Day 1, fecal swab, whole body study A
M11Fcsw M1, Day 1, fecal swab, whole body study A
M31Plmr M3, Day 1, right palm, whole body study A
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Hesham999666
commented on June 3, 2024
Yes. It is same your format, despite I don't have Phylogenetic Tree in my data
I have two 2 variables, one of them sample_x (repeated SampleID)
head(sample_data(physeq))
Sample_x SampleType
1001SH 1001SH CFH
......
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guokai8
commented on June 3, 2024
Could you share part of your data? so I can test
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Hesham999666
commented on June 3, 2024
I have send to your email four days ago hope that you received.
I try it to uploaded here but it doesn't work.
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guokai8
commented on June 3, 2024
Hi,
I got the data. But there are some errors when I load the data:
> load("heshampig_bacteria_phyloseq.rds")
Error in load("heshampig_bacteria_phyloseq.rds") :
bad restore file magic number (file may be corrupted) -- no data loaded
In addition: Warning messages:
1: In readChar(con, 5L, useBytes = TRUE) :
truncating string with embedded nuls
2: file ‘heshampig_bacteria_phyloseq.rds’ has magic number 'X'
Use of save versions prior to 2 is deprecated
I am not sure how you save the data. You can just save your data by using
save(physeq,file="physeq.rdata",compress=T)
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Hesham999666
commented on June 3, 2024
Hi Kai
I sent to your [email protected] by Mar 18, 2021, 10:09 PM
I have a replied to your "Could you share part of your data? so I can test" I sent it but the file was big,
So I sent it by your personal email (Gmail).
BUT Actually it is working for me now, when I am upload the microbial package before the phyloseq package.
lefese analysis for microbiome data
upload the libraries
library(microbial)
library(phyloseq)
upload the phyloseq files
ps1 <- readRDS ("heshamcow_bacteria_phyloseq.rds")
ps2 <- readRDS ("heshampig_bacteria_phyloseq.rds")
merge phyloseqs =
airmicrobiome <- merge_phyloseq (ps1, ps2)
add metadta to your merged phyloseq file
metadata <- read.csv("cowandpigmetadata_x.csv", sep =',', header=TRUE, row.names=1)
sample_data(airmicrobiome) <- metadata
performe the lefese on phyloseq
res <- ldamarker(airmicrobiome,group="SampleType")
plotLDA(res,group=c("CFH","PFH"),lda=5,pvalue=0.05, color = c("red","green"),fontsize.x = 7,fontsize.y = 8)
plotLDA(res,group=c("CFH","SUH"),lda=5,pvalue=0.05, color = c("red","green"),fontsize.x = 7,fontsize.y = 8)
plotLDA(res,group=c("PFH","SUH"),lda=5,pvalue=0.05, color = c("red","green"),fontsize.x = 7,fontsize.y = 8)
Thanks Kai
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guokai8
commented on June 3, 2024
OK. I got it. Glad it works for you.
Kai
from microbial.
Related Issues (8)
- Citation HOT 1
- Blank plot for plotLDA() HOT 17
- ldamarker output table HOT 1
- lda plot for more than 2 groups HOT 1
- ldamarker error HOT 6
- Rearrange sample in Taxonomy plot based on groups HOT 4
- Taxa labels for plotLDA
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