regarding heatmap

[divyapr...@gmail.com]

Hi every body 

I am generating heat map in a PDF file but i am not able to visualize it properly after opening the file,. and secondly i want to give some other color to the heatmap.

For convenience i am attaching the file.

[divyapr...@gmail.com]

Please help me out here

[divyapr...@gmail.com]

Hi 

Please any one  help me out here

[Kyle Bittinger]

Could you send the command you used to generate the heatmap, and any commands you used to prepare the input files?

I may ask for examples of your input files, which you can post or send privately, as you prefer.

Best,

Kyle

[divyapr...@gmail.com]

Hi Kyle 

this is the command that i am running. 

make_otu_heatmap.py -i Soil_otus/otu_table.biom -o heat_map and i have also attached the pdf file.

[Kyle Bittinger]

Have you tried some of the options listed in the documentation?

http://qiime.org/scripts/make_otu_heatmap.html

For readability, you might increase the PDF height with "--height 15".  As for the color, you might pass "--color_scheme GnBu" as an option.

[divyapr...@gmail.com]

Hi Kyle 

please mention here how to increase the PDF height with --- height 15.

[divyapr...@gmail.com]

Hi please help me here also 

I have posted some of the queries. Being new to Qiime i am not able to do filtering. i mean i don't know whether i have to run filter_otus_from_otu_table.py or   filter_samples_from_otu_table.py or filter_taxa_from_otu_table.py.

I have got three samples, with otu count 3412. what is the better option for me . So that i can proceed forward to prepare phylogenetic tree and heatmap and can do other analysis. 

More over i want to known after filtering with which file i have to proceed with.

For convenience i am attaching the summarized biom file. 

[Kyle Bittinger]

You want filter_otus_from_otu_table.py

As for the PDF height, you should literally add the characters " --height 15 " to the make_otu_heatmap.py command.