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umerijaz / microbiomeSeq

An R package for microbial community analysis in an environmental context
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Error in plot.ordination #30

Open giriarteS opened 5 years ago

giriarteS commented 5 years ago

Everything was working fine but now the plot.ordination function is showing the following error:

plot.ordination(ord.res2, method="PCoA", pvalue.cutoff=0.05, show.pvalues=T) Error in ordiellipse(sol, groups, display = "sites", kind = "se", conf = 0.95, : could not find function "ordiellipse"

marasodi commented 4 years ago

Hi please assist, I ran this and I got the error below p <- plot.ordination(ord.res, method="NMDS", pvalue.cutoff=0.05, show.pvalues=T)

ERROR:[1] groups p_value label

<0 rows> (or 0-length row.names) Error in `$<-.data.frame`(`*tmp*`, "p_label", value = "p-value= ") : replacement has 1 row, data has 0
AlfredUg commented 4 years ago

Heya @marasodi, you may consider changing the cut off p-value. This error may be a result of having no significant results at as per the chosen cut-off pvalue.

marasodi commented 4 years ago

thanks, one more question with regards to the plot anova function in alpha diversity measures. On the csv file output for example if on the csv we have this output 1,"Simpson","A","B","1.0686286211328","0.043" does 1.0686286211328 represents the degree of confidence(df)?

marasodi commented 4 years ago

and also on the differential _abundance function in DESeq2 the output

f__Aureobasidiaceae,16.5124755168758,-2.92458476941722,3.00272909969888e-05,0.000120109163987955,"A", does 16.5124755168758 represents degree of confidence? Thanks in advance