January 24, 2023 - Correct sampleIDs

Changed sampleIDs for the healthy donor samples from "ht-###-##" to "hd-###-##"
DFI-Bioinformatics · Jan 24, 2023 · b621bff · b621bff
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commit b621bff
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Showing 35 changed files with 38 additions and 38 deletions.
diff --git a/Data/LT_Modeling.RData b/Data/LT_Modeling.RData
diff --git a/Data/metab_qual_anon.rds b/Data/metab_qual_anon.rds
diff --git a/Data/metab_quant_anon.rds b/Data/metab_quant_anon.rds
diff --git a/Data/metaphlan_anon.rds b/Data/metaphlan_anon.rds
diff --git a/Data/sample_lookup.rds b/Data/sample_lookup.rds
diff --git a/Microbiome_Liver_Transplant_Manuscript.Rmd b/Microbiome_Liver_Transplant_Manuscript.Rmd
@@ -518,7 +518,7 @@ pirate_colors <- c("#1A49BE", "#3A001E")
 pirate_colors2 <- c("#3A001E", "#3A001E", "#3A001E", "#1A49BE")
 
 t_metaphlan <- metaphlan_df %>%
-  filter(sampleID %in% first_samps$sampleID| grepl(sampleID, pattern = "ht")) %>% 
+  filter(sampleID %in% first_samps$sampleID| grepl(sampleID, pattern = "hd")) %>% 
   mutate(db = ifelse(grepl(sampleID, pattern = "lt"), "Liver Transplant", "Healthy Donor")) %>% 
   select(sampleID, taxid, db, pctseqs, Total) %>% 
   group_by(sampleID, taxid, pctseqs) %>% 
@@ -2823,7 +2823,7 @@ text(
 ### Potential Figure 6A: sPLS-DA Diversity Groups and Healthy Donors using Qualitative Metabolomics
 ```{r, potential-figure-6A-splsda-diversity-groups, fig.dim = c(16, 12), message=FALSE, warning=FALSE}
 diversity_healthy_metab_mat <-
-  metab_qual_anon %>% filter(sampleID %in% first_samps$sampleID|grepl(patientID, pattern = "ht")) %>% 
+  metab_qual_anon %>% filter(sampleID %in% first_samps$sampleID|grepl(patientID, pattern = "hd")) %>% 
   mutate(compound = ifelse(compound == "isovaleric-acid", "isovalerate", compound),
          compound = str_to_title(compound)) %>%
   filter(compound %in% heatmap_cmpds$compound|is.na(compound)) %>%

diff --git a/Microbiome_Liver_Transplant_Manuscript.html b/Microbiome_Liver_Transplant_Manuscript.html
diff --git a/Results/Figure_1.pdf b/Results/Figure_1.pdf
diff --git a/Results/Figure_1A.pdf b/Results/Figure_1A.pdf
diff --git a/Results/Figure_1B.pdf b/Results/Figure_1B.pdf
diff --git a/Results/Figure_1C.pdf b/Results/Figure_1C.pdf
diff --git a/Results/Figure_1D.pdf b/Results/Figure_1D.pdf
diff --git a/Results/Figure_1E.pdf b/Results/Figure_1E.pdf
diff --git a/Results/Figure_1F.pdf b/Results/Figure_1F.pdf
diff --git a/Results/Figure_1G.pdf b/Results/Figure_1G.pdf
diff --git a/Results/Figure_1H.pdf b/Results/Figure_1H.pdf
diff --git a/Results/Figure_1I.pdf b/Results/Figure_1I.pdf
diff --git a/Results/Figure_1J.pdf b/Results/Figure_1J.pdf
diff --git a/Results/Figure_2.pdf b/Results/Figure_2.pdf
diff --git a/Results/Figure_3.pdf b/Results/Figure_3.pdf
diff --git a/Results/Figure_4A.pdf b/Results/Figure_4A.pdf
diff --git a/Results/Figure_4B.pdf b/Results/Figure_4B.pdf
diff --git a/Results/Figure_4C.pdf b/Results/Figure_4C.pdf
diff --git a/Results/Figure_5A.pdf b/Results/Figure_5A.pdf
diff --git a/Results/Figure_5B.pdf b/Results/Figure_5B.pdf
diff --git a/Results/Figure_6.pdf b/Results/Figure_6.pdf
diff --git a/Results/Figure_6A.pdf b/Results/Figure_6A.pdf
diff --git a/Results/Figure_6B.pdf b/Results/Figure_6B.pdf
diff --git a/Results/Potential_Figure_6A.pdf b/Results/Potential_Figure_6A.pdf
diff --git a/Results/Potential_Supplemental_Figure_2.pdf b/Results/Potential_Supplemental_Figure_2.pdf
diff --git a/Results/Supplemental_Figure_2.pdf b/Results/Supplemental_Figure_2.pdf
diff --git a/Results/Supplemental_Figure_3.pdf b/Results/Supplemental_Figure_3.pdf
diff --git a/Results/Supplemental_Figure_4.pdf b/Results/Supplemental_Figure_4.pdf
diff --git a/Results/enterococcus_expansion_boxplot.pdf b/Results/enterococcus_expansion_boxplot.pdf
diff --git a/Results/microbiota_table.csv b/Results/microbiota_table.csv