Add gene labels on Volcano markerPlot

[tzhu-bio]

Is there an easy way to add gene labels on Volcano markerPlot?

[rcorces]

We do not provide code to do this. you would have to do this manually

[NoemieL]

Hi, I am also interested to do this. Where or how could we find/get the data (gene list of the colored dots)to do it? Thanks

[rcorces]

from the SummarizedExperiment objects output by various ArchR functions such as getMarkerFeatures()

[NoemieL]

Thanks. I did not get the name of the gene when I used getMarker() after getMarkerFeatures(). Do you have any idea why?

markerTest_C11_C12<- getMarkerFeatures(
ArchRProj = ArchRProj,
useMatrix = "PeakMatrix",
groupBy = "Clusters2",
testMethod = "wilcoxon",
bias = c("TSSEnrichment", "log10(nFrags)"),
useGroups = "C11",
bgdGroups = "C12"
)

getMarkers(markerTest_C11_C12, cutOff = "FDR <= 0.05 & Log2FC >= 1")$C11
DataFrame with 6515 rows and 7 columns
seqnames idx start end Log2FC FDR MeanDiff

74122 chr19 505 1607211 1607711 3.99734 2.55652e-30 0.292120
25173 chr11 1043 8634439 8634939 4.43359 1.35060e-24 0.263550
137311 chr6 6743 116631404 116631904 4.03947 6.72648e-22 0.210086
148203 chr8 345 11429851 11430351 3.12054 1.82864e-19 0.171053
18771 chr10 2244 34674123 34674623 3.33251 1.23828e-18 0.187013
... ... ... ... ... ... ... ...
43283 chr13 586 32414952 32415452 2.99563 0.0499483 0.0274050
47838 chr14 2183 64976615 64977115 2.64981 0.0499483 0.0171076
151266 chr8 3408 69858608 69859108 2.69518 0.0499483 0.0189222
31704 chr11 7574 109155211 109155711 1.26343 0.0499497 0.0413292
29736 chr11 5606 71120524 71121024 1.60546 0.0499748 0.0403996

[rcorces]

the idx column should match the index from your peakSet which contains the name of the closest gene. Otherwise you would map to peakToGeneLinks or coaccessibility