search

joey711 / shiny-phyloseq

An interactive web application for demonstrating and using phyloseq.
http://joey711.github.io/shiny-phyloseq
GNU General Public License v3.0
60 stars 45 forks source link

Can't color samples in ordination plot #50

Closed mlangill closed 9 years ago

mlangill commented 10 years ago

I have tried a couple of different datasets where there is just one qualitative grouping for the samples (3 groups). I can colour by samples using this metadata for all of the plots EXCEPT the ordination plots. I keep getting this error in the terminal:

Warning in plot_ordination(physeq = physeq_ord(), ordination = get_ord(),  : 
Color variable was not found in the available data you provided.No color mapped.
No available covariate data to map on the points for this plot `type`
joey711 commented 10 years ago

Hi Morgan, sorry for the trouble,

Can you list what version of phyloseq you are using? Also, you'll note that the ordination can display OTUs, samples, or both. Which were you selecting? The widget should automatically display available options if they're there, and they should only be there if the variables are in your data. Mind sharing a little more detail about the steps you took?

joey

mlangill commented 10 years ago

Seems to be something related to my specific OTU table: https://www.dropbox.com/s/bt5h1fibgzon2hh/otu_table_with_sample_metadata.biom?dl=0

ckcollings commented 9 years ago

I'm having the same problem. I do not know how to get colors.

unweighted_UniFrac_distance_matrix ABiochar1 AControl2 ABiochar3 ABiochar2 AControl1 AControl2 0.6027745
ABiochar3 0.6078315 0.6177005
ABiochar2 0.6003199 0.5476134 0.6193400
AControl1 0.5856539 0.5679646 0.5851082 0.5661961
AControl3 0.6070889 0.5432251 0.6268210 0.5595632 0.5699145

iMDS <- ordinate(data2, "MDS", distance = unweighted_UniFrac_distance_matrix) plot_ordination(data2, iMDS, type = "samples", color = "Treatment") No available covariate data to map on the points for this plot type Warning message: In plot_ordination(data2, iMDS, type = "samples", color = "Treatment") : Color variable was not found in the available data you provided.No color mapped.

data2 phyloseq-class experiment-level object otu_table() OTU Table: [ 57783 taxa and 6 samples ] sample_data() Sample Data: [ 6 samples by 1 sample variables ] tax_table() Taxonomy Table: [ 57783 taxa by 7 taxonomic ranks ] phy_tree() Phylogenetic Tree: [ 57783 tips and 57781 internal nodes ]

sample_data(data2) Sample Data: [6 samples by 1 sample variables]: Treatment ABiochar1 Biochar AControl2 Control ABiochar3 Biochar ABiochar2 Biochar AControl1 Control AControl3 Control

head(otu_table(data2)) OTU Table: [6 taxa and 6 samples] taxa are rows ABiochar1 AControl2 ABiochar3 ABiochar2 AControl1 AControl3 New.ReferenceOTU99252 0 0 1 0 0 1 New.ReferenceOTU30910 1 0 5 0 4 0 New.ReferenceOTU55833 0 0 10 0 2 0 New.ReferenceOTU242194 0 0 2 0 1 0 New.ReferenceOTU384960 0 0 1 0 1 0 New.ReferenceOTU497495 0 0 1 0 0 1

joey711 commented 9 years ago

I cannot reproduce this bug. Will close for now. The latest version of shiny-phyloseq should show color mapping that works for ordination panel.