SEQanswers what is the name of this kind of graph and how to plot?
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10-02-2011, 05:16 AM   #1
tianyub836
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Location: China

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what is the name of this kind of graph and how to plot?

Do anyone know about the graph attached and how to plot it ?
any packages?

thanks
Attached Images
 Wu-2010-Whole genome wide ex.jpg (79.1 KB, 257 views)

 10-02-2011, 08:31 AM #2 vebaev Senior Res.   Location: Plovdiv, Bulgaria Join Date: Oct 2008 Posts: 110 It is a scatterplot, you can make one as plotting normalized values from 2 samples by log10 scale. But most probably you will have difficulties making coloring by condition (your log2ratio for deregulated genes ) in simple software like Excel. __________________ ------------ SMART - bioinfo.uni-plovdiv.bg Last edited by vebaev; 10-02-2011 at 08:33 AM.
 10-02-2011, 12:56 PM #3 upendra_35 Senior Member   Location: USA Join Date: Apr 2010 Posts: 102 This plot is basically for visualising DGE results and it is called upon by using plotSmear function in edgeR. I have copied the text from edgeR for better understanding. "The function plotSmear can be used to generate a plot of the log-fold change against the log- concentration for each tag (analogous to an MA-plot in the microarray context). We can easily identify the top DE tags and highlight them on the plot. The code for producing the default fold-change plot is shown below, and the result of this code is shown in Figure 2. > detags264 <- rownames(topTags(de.com, n = 264)\$table) > plotSmear(d, de.tags = detags264, main = "FC plot using common dispersion") > abline(h = c(-2, 2), col = "dodgerblue")" I kind of like this plot but i still don't know how to use different colors for different things. I hope this info helps
10-03-2011, 05:26 AM   #4
tianyub836
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Location: China

Join Date: Apr 2011
Posts: 23

Quote:
 Originally Posted by upendra_35 This plot is basically for visualising DGE results and it is called upon by using plotSmear function in edgeR. I have copied the text from edgeR for better understanding. "The function plotSmear can be used to generate a plot of the log-fold change against the log- concentration for each tag (analogous to an MA-plot in the microarray context). We can easily identify the top DE tags and highlight them on the plot. The code for producing the default fold-change plot is shown below, and the result of this code is shown in Figure 2. > detags264 <- rownames(topTags(de.com, n = 264)\$table) > plotSmear(d, de.tags = detags264, main = "FC plot using common dispersion") > abline(h = c(-2, 2), col = "dodgerblue")" I kind of like this plot but i still don't know how to use different colors for different things. I hope this info helps
thanks, upendra_35
but i thought the function plotSmear in edgeR is not capable of plotting the graph i have attached but the graph i attached this time.

correct me if i am wrong
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 result.png (21.4 KB, 45 views)

 10-03-2011, 02:48 PM #5 upendra_35 Senior Member   Location: USA Join Date: Apr 2010 Posts: 102 As far as i know plotSmear can only plot the first plot you have attached. I don't know much about the second plot, but i guess it is other way of representing DGE (red indicates Non-DE genes, black indicates under expressed and pink indicates over expressed genes). Where did you get this plot anyway?
10-03-2011, 06:05 PM   #6
tianyub836
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Location: China

Join Date: Apr 2011
Posts: 23

Quote:
 Originally Posted by upendra_35 As far as i know plotSmear can only plot the first plot you have attached. I don't know much about the second plot, but i guess it is other way of representing DGE (red indicates Non-DE genes, black indicates under expressed and pink indicates over expressed genes). Where did you get this plot anyway?
well, upendra_35, thanks,.

the first graph i attached is from a paper has been published and the second one was generated from R package DEGseq.

i have read the edgeR manual and the examples and found the plotSmear function in the manual and graph in the example are more like the second graph i have attached.

by the way, red ones in the second one mean DEGs and pink ones mean expressed genes that do not meet the threshold of p value and changefold i have set and the black ones are non-DEGs.

 10-04-2011, 12:48 PM #7 upendra_35 Senior Member   Location: USA Join Date: Apr 2010 Posts: 102 Thanks tianyub836 for the info. Much appreciated........