flip plot from plotSignal

[RobTesf]

Hello, I was wondering is there an option to flip the line plots of plotSignal(). I have two bigwig tracks of signals from forward and reverse strands and I would like to plot them one on top of the other with the reverse strand signal having upside-down y axis. It's similar to what you propose with fill argument able to take a "strand" information when reading bed files using plotRanges(). I believe the option of angle in viewport() could do the trick, and I tried to fix it by tweaking your files but have problems finding the accessory functions... Thanks in advance for the time

[nekramer]

Hello!

There is actually a built-in way to plotSignal() to plot two signals together, with one reflected over the x-axis. Since your data is already split by strand, you can input both files to plotSignal() as a list(), with the forward strand signal listed first to be in the positive y-axis. You can also input two different colors to fill and/or linecolor to have each strand signal colored differently. Here's an example:

library(plotgardener)
#> 
#> Attaching package: 'plotgardener'
#> The following object is masked from 'package:base':
#> 
#>     c
library(plotgardenerData)
data("IMR90_ChIP_H3K27ac_signal")
data("GM12878_ChIP_H3K27ac_signal")

pageCreate(width = 7.5, height = 2)

region <- pgParams(
    chrom = "chr21",
    chromstart = 28000000, chromend = 30300000,
    assembly = "hg19"
)

plotSignal(data = list(GM12878_ChIP_H3K27ac_signal, 
                       IMR90_ChIP_H3K27ac_signal),
           params = region,
           x = 0.5, y = 0.25, 
           linecolor = c("blue", "red"),
           fill = c("blue", "red"),
           width = 6.5, height = 1.5)
#> signal[signal1]

^{Created on 2023-07-21 with reprex v2.0.2}

I hope this helps!

Best, Nicole

[RobTesf]

works like a charm. Thanks a lot for the quick response. I have a potential bug report though in plotMultiSignal(). range argument does not seem to be taken into consideration with this function:

library("plotgardenerData")
data("GM12878_ChIP_CTCF_signal")
data("IMR90_ChIP_CTCF_signal")
data("GM12878_ChIP_H3K27ac_signal")
data("IMR90_ChIP_H3K27ac_signal")
library("RColorBrewer")

## List of multiple signal datasets
signalList <- list(GM12878_ChIP_CTCF_signal, GM12878_ChIP_H3K27ac_signal, 
    IMR90_ChIP_CTCF_signal, IMR90_ChIP_H3K27ac_signal)

## Create page
pageCreate(width = 6.9, height = 3.5, default.units = "inches")

## Plot multiple signals
multisignal <- plotMultiSignal(signalList, chrom = "chr21",
                               chromstart = 28150000, chromend = 29150000,
                               linecolor = c(brewer.pal(n = 9,"YlGnBu")[4],
                                             brewer.pal(n = 9,"YlGnBu")[5],
                                             brewer.pal(n = 9,"YlGnBu")[6],
                                             brewer.pal(n = 9,"YlGnBu")[7]),
                               label = c("GM12878 CTCF", "GM12878 H3K27ac",
                                         "IMR90 CTCF", "IMR90 H3K27ac"),
                               assembly = "hg19",
                               x = 0.2, y = 0.2,
                               width = 6.5, height = 3,
                               default.units = "inches",
                               gapdistance = 0.1)

## Create page
pageCreate(width = 6.9, height = 3.5, default.units = "inches")

## Plot multiple signals
multisignal <- plotMultiSignal(signalList, chrom = "chr21",
                               chromstart = 28150000, chromend = 29150000,
                               linecolor = c(brewer.pal(n = 9,"YlGnBu")[4],
                                             brewer.pal(n = 9,"YlGnBu")[5],
                                             brewer.pal(n = 9,"YlGnBu")[6],
                                             brewer.pal(n = 9,"YlGnBu")[7]),
                               label = c("GM12878 CTCF", "GM12878 H3K27ac",
                                         "IMR90 CTCF", "IMR90 H3K27ac"),
                               assembly = "hg19",
                               x = 0.2, y = 0.2,
                               width = 6.5, height = 3,
                               default.units = "inches",
                               gapdistance = 0.1,range=c(0,500))

These 2 commands give the exact same plot...

[nekramer]

Ah yes, the range parameter for plotMultiSignal is a bit misleading; plotMultiSignal internally calculates the best range for all the signals and currently overrides any user-defined range. I'll work on clarifying this. Thanks for pointing this out!

Nicole