search

franciscolobo / KOMODO2

Annotation based, phylogeny aware comparative genomics tool
GNU General Public License v2.0
0 stars 4 forks source link

warning needed when nothing passes the filter #6

Open g1o opened 4 years ago

g1o commented 4 years ago

After make_correlation_plot.R, table.Rmd will fail if there is nothing.

idx <- which(

q-value cutoffs

(plotframe$corrected_contrasts < defs$linear_model.qvalue.cutoff) &
  (plotframe$Spearman_qvalue   < defs$spearman.qvalue.cutoff) &
  (plotframe$Pearson_qvalue    < defs$pearson.qvalue.cutoff) &
  (plotframe$Kendall_qvalue    < defs$kendall.qvalue.cutoff) &
  # correlation cutoffs
  ((plotframe$Pearson_cor  > defs$pearson.cor.upper.cutoff)  | (plotframe$Pearson_cor  < defs$pearson.cor.lower.cutoff)) &
  ((plotframe$Spearman_cor > defs$spearman.cor.upper.cutoff) | (plotframe$Spearman_cor < defs$spearman.cor.lower.cutoff)) &
  ((plotframe$Kendall_cor  > defs$kendall.cor.upper.cutoff)  | (plotframe$Kendall_cor  < defs$kendall.cor.lower.cutoff)) &
  # basic statistics cutoffs
  (plotframe$size              > defs$annotation_size.cutoff) &
  (plotframe$prevalence        > defs$prevalence.cutoff) &
  (plotframe$heterogeneity     > defs$heterogeneity.cutoff) &
  (plotframe$sd                > defs$sd.cutoff) &
  (plotframe$cv                > defs$cv.cutoff))