What'S Wrong With Heatmap.2, Heatmap Turns To Blue After Finishing Plotting

Question

[Ming Tommy Tang]

Hi everyone,

I asked in Seqanwser, try my luck here.

I was plotting a transcription factor ChIP-seq data at TSS with heatmap.2

http://s24.postimg.org/njywavo7p/Selection_015.png

the problem is that the plot becomes blue after plotting as the green-red colour setting. if you resize the window, you can see the red signal enriched at the TSS, but once finished plotting, the blue spread to the whole figure and I could not see anything...

See the picture above.

what's wrong with heatmap.2?

Thanks

Answer 1

[Steve Lianoglou]

There is nothing wrong with heatmap.2, you just have to take a minute to read through its documentation.

You are particularly interested in the trace argument, which has the following documentation associated to it:

trace: character string indicating whether a solid "trace" line
       should be drawn across 'row's or down 'column's, 'both' or
       'none'.  The distance of the line from the center of each
       color-cell is proportional to the size of the measurement.
       Defaults to 'column'.

You want to set that to none. The very next help item is for tracecol:

tracecol: character string giving the color for "trace" line. Defaults
          to "cyan".

Which might have been helpful in identifying trace as the culprit since it sets the default color to "cyan", which is the color that's eating the heatmap after it's plotted.

[Ming Tommy Tang]

Thanks! I do need to put the argument trace="none". you saved me.... I should have read more documentation. Thanks again!