Align-GVGD scores for SNP values

Question

[garimav89]

How to plot Align-GVGD scores for SNPs in Gene by using ggplot2?

I want to construct a map for values(EXAMPLE) below:

id  gv_scores(X) gd_scores(Y)     class
1   0            44.5             C45
2   0            92.5             C65
3   0            82.3             C65

Help will be appreciated

[Steven Lakin]

So do you want an x-y scatter plot separated by color? Or separate scatter plots for each class? Or something else? There is a lot you can do with ggplot2.

[garimav89]

I want an x-y scatter plot separated by colour. Actually my X values are always 0 for every id so now I want to represent my data from a new table (example lies below)

id(y)   pos(x)    gd         class
1       35        94.3       C65
2       67        45.6       C15
3       79        83.9       C65

I want tile plot in which my gd values are written inside tiles of colours according to class.

Somewhat like the map below

Answer 1

[Steven Lakin]

Based on what you've said above, this should work:

library(ggplot2)
g <- ggplot(data=yourDataFrame, aes(pos, id))
g + geom_tile(aes(fill=class)) + geom_text(aes(label=gd))

So for example:

testDataFrame <- data.frame("id" = c(1,2,3), "pos" = c(35,67,79), "gd" = c(94.3,45.6,83.9), "class" = c("C65", "C15", "C65"))
g <- ggplot(data=testDataFrame, aes(pos, id))
g + geom_tile(aes(fill=class)) + geom_text(aes(label=gd))

That will give you a heatmap similar to what you described above while using your x/y values.

Edit: changed text label to gd

[garimav89]

Thank you Steven, it worked

But I need a colour gradient for class column and also a defined limits for x-axis

I'm using following code:

g <- g+ scale_fill_gradient (low = "white" , high = "red")

This is not working. Please help me

[Steven Lakin]

If you could accept the answer using the buttons on the left of my post, that'd be great. The site works best when answered questions are marked.