Suspect that this is easier than I realize, but taking some figuring out
currently. Any help would be appreciated.
I have a data frame (testhm) with many rows such as:
ProbeSet.ID.F ProbeSet.ID Feature.ID G.S X0030V120810.14 X0143V120110.14
X0258V111710.14 X0283V111710.14 X0430V120710.14 X0472V111610.14
X0520V111610.14 X0546V113010.14 X0578V111810.14 X0624V111810.14
2 7892501_943979 7892501 943979 --- 33
52 18 34 5 49
81 20 90 44
3 7892501_493089 7892501 493089 --- 35
8 13 5 5 8
7 10 7 34
I would like to plot density or dot plots for each of the values in a row,
but to group the plots such as those rows with a common ProbeSet.ID are
plotted on the same axes.
So each individual point in rows with sharing the ProbeSet.ID
"7892501"
would all be plotted on the same chart, and then for a new ProbeSet.ID a new
chart is plotted. There are generally 15-20 rows per unique ProbeSet.ID.
So far I can plot rows, but the upfront grouping is causing a headache.
pdf(file = "density_cd.pdf")
par(mfrow=c(4,4))
for (i in 1:nrow(testhm)){
plot(density(testhm[i,]))
}
dev.off()
I'd be grateful for any advice on this.
Thanks.
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In terms of a reproducible example:
ProbeSet.ID.F ProbeSet.ID Feature.ID Gene.Symbol X0030V120810.4
X0143V120110.4 X0258V111710.4 X0283V111710.4 X0430V120710.4 X0472V111610.4
X0520V111610.4 X0546V113010.4 X0578V111810.4 X0624V111810.4
7896741_479302 7896741 479302 OR4F17 20
14 5 4 43 85
12 14 7 5
7896741_226901 7896741 226901 OR4F17 15
73 31 14 32 28
10 42 11 28
7896741_2337 7896741 2337 OR4F17 168
126 111 120 119 84
149 76 347 88
7896741_289201 7896742 289201 OR4F18 54
64 11 6 59 66
10 50 51 27
7896741_240730 7896742 240730 OR4F18 38
158 95 38 59 131
114 100 102 40
7896741_776611 7896743 776611 OR4F19 6
27 7 7 16 105
35 17 19 23
...becomes three panels of a plot, containing the lines:
Plot 1:
7896741_479302 7896741 479302 OR4F17 20
14 5 4 43 85
12 14 7 5
7896741_226901 7896741 226901 OR4F17 15
73 31 14 32 28
10 42 11 28
7896741_2337 7896741 2337 OR4F17 168
126 111 120 119 84
149 76 347 88
Plot2:
7896741_289201 7896742 289201 OR4F18 54
64 11 6 59 66
10 50 51 27
7896741_240730 7896742 240730 OR4F18 38
158 95 38 59 131
114 100 102 40
Plot 3:
7896741_776611 7896743 776611 OR4F19 6
27 7 7 16 105
35 17 19 23
and so on...
Any ideas much appreciated.
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