dbRDA plot question

[Marilou]

Hi,

I am using dbRDA to compare categories and plots and stats have been successfully generated.  The plot however contains sample labels instead of markers (that denote samples). Is there a way to change the sample labels in the plot with markers of different colors (representing samples). I am using MacQiime 1.8 and using the jacknifed matrix and I have attached files below.

compare_categories.py --method dbrda -i jacknifed_blasted/unweighted_unifrac_otu_table.blasted.txt -m BC7Map1.txt -c Resistotype_all -o jack_dbrda/dbrda/unweighted/Resistotype_all -n 999

Thanks in advance for the help.

Best,
marilou

[Jai Ram Rideout]

Hi Marilou,

Unfortunately there isn't a way to customize the db-RDA plots generated by compare_categories.py. The scripts uses R's vegan::capscale function to generate the plot. You may be able to customize the plot by running the analysis directly in R instead of using compare_categories.py. Here's the R script that compare_categories.py is running in case you want to use this as a starting point.

Hope this helps,

Jai

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[Sophie]

Thanks Jai! Mailou - if you want to dig a bit more into the R, here's a response written by my colleague Jorge:

I think vegan decides to switch from text to points as the number of samples increases.

To force having points, it's necessary to modify the R code that runs the analysis (qiime/support_files/R/dbrda.r), replacing its last line:

plot(capscale.results, display=c("wa", "bp"))

with the following lines:

plot(capscale.results, display="wa", type="point")
text(capscale.results, col="blue", display="bp")

Moreover, if Marilou wants to color the samples according to the Resistotype_all column, it's possible to do so by eg doing this instead:

# More colors in http://www.stat.columbia.edu/~tzheng/files/Rcolor.pdf

colors <- c("coral", "coral4", "mediumblue", "darkgoldenrod2",
            "darkolivegreen3", "darkorchid1", "red2")

# Plot nothing, but get the figure

plot(capscale.results, type="none")

# Now plot samples, coloured by the factors in the column (-c option to script)

points(capscale.results, display ="wa", col=colors[factor],
      pch=21, bg=colors[factor])

# And arrows for factors

text(capscale.results, col="blue", display="bp")

# Include a legend that doesn't clash with points

legend("bottomleft", legend=levels(factor), bty="n",
       col=colors, pch=21, pt.bg=colors)

In general, it's possible to heavily customize ordination plots, but it's not really easy...

The plot we get is attached.

Thanks,

Sophie

[Jai Ram Rideout]

Thanks Sophie and Jorge!

[Marilou]

Jai, Sophie, Jorge,

I would like to say thank you for this (albeit late!). I realized that I did not get into thanking you guys. Your suggestion (about customizing colors) below works and I got to customized my dbRDA plots. You guys are awesome. (:>)

Marilou

[Jai Ram Rideout]

Glad to hear you got it working!

Jai