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garridoo · Mar 11, 2021 · e8f72f7 · e8f72f7
1 parent 0cb634b
commit e8f72f7
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Showing 2 changed files with 7 additions and 1 deletion.
diff --git a/scripts/IPL.R b/scripts/IPL.R
@@ -18,6 +18,12 @@ otu_table_norm_At_NC <- apply(otu_table_At_NC, 2, function(x) x/sum(x))
 otu_table_norm_Cr_NC <- apply(otu_table_Cr_NC, 2, function(x) x/sum(x))
 otu_table_norm_Cr_MC <- apply(otu_table_Cr_MC, 2, function(x) x/sum(x))
 
+# remove OTUs with zero counts
+
+idx <- rowSums(otu_table_CrIPL) > 0
+otu_table_CrIPL <- otu_table_CrIPL[idx, ]
+otu_table_norm_CrIPL <- otu_table_norm_CrIPL[idx, ]
+
 # remove wells without a insufficient number of reads
 
 min_reads <- 100

diff --git a/scripts/IPL_recovery_rates.R b/scripts/IPL_recovery_rates.R
@@ -94,7 +94,7 @@ recovery <- function(otu_table_norm_IPL, otu_table_norm_NC, host_IPL, host_NC, t
 
     ggsave(paste(figures.dir, "recovery_cumsum_", host_IPL, host_NC, ".pdf", sep=""), p,
            width=width_rec_barplot, height=height_rec_barplot)
-print(df_top$cumsum[100])
+
 }
 
 cat("\nRecovery rates for CrIPL respect to At roots:\n\n")