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

[tianyub836]

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

thanks

[vebaev]

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.

[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

[tianyub836]

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

[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?

[tianyub836]

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.

[upendra_35]

Thanks tianyub836 for the info. Much appreciated........