英文:
How to add conditional annotation from other column of R dataframe in ggplot2
问题
I will translate the code part as requested:
我正在尝试从包含超过300k行的数据框中制作一个图表，其中Y的高值和低值将从另一列而不是X和Y中的数据进行注释。我该怎么做..!!数据框：chr start end.x StoZ.x Hscore end.y StoZ.y Tier Gene1 chr1 1 10000 0.0000000 0 NA NA <NA> <NA>2 chr1 10001 20000 3.6488202 2 NA NA <NA> <NA>3 chr1 20001 30000 -0.8475483 0 NA NA <NA> <NA>4 chr1 30001 40000 2.1279359 2 NA NA <NA> <NA>5 chr1 40001 50000 1.4119515 0 NA NA <NA> <NA>................................................256 chr1 2550001 2560000 -2.363378 1 2560000 -2.363378 T1 TNFRSF14257 chr1 2560001 2570000 -0.796173 0 2570000 -0.796173 T1 TNFRSF14................................................305 chr1 3040001 3050000 0.0564608 0 NA NA NA NA306 chr1 3050001 3060000 1.4822029 0 NA NA NA NA307 chr1 3060001 3070000 1.7718186 0 3070000 1.7718186 T1 PRDM16308 chr1 3070001 3080000 1.5650776 0 3080000 1.5650776 T1 PRDM16................................................
The translation of the code snippet is complete. If you have any more specific questions or need further assistance, please feel free to ask.
英文:
I'm trying to make a plot from a dataframe of over 300k rows where the high and low values of Y will be annotated from another column rather than the x and y.
How can I do that..!!
Dataframe :
chr start end.x StoZ.x Hscore end.y StoZ.y Tier Gene1 chr1 1 10000 0.0000000 0 NA NA <NA> <NA>2 chr1 10001 20000 3.6488202 2 NA NA <NA> <NA>3 chr1 20001 30000 -0.8475483 0 NA NA <NA> <NA>4 chr1 30001 40000 2.1279359 2 NA NA <NA> <NA>5 chr1 40001 50000 1.4119515 0 NA NA <NA> <NA>................................................256 chr1 2550001 2560000 -2.363378 1 2560000 -2.363378 T1 TNFRSF14257 chr1 2560001 2570000 -0.796173 0 2570000 -0.796173 T1 TNFRSF14................................................305 chr1 3040001 3050000 0.0564608 0 NA NA NA NA306 chr1 3050001 3060000 1.4822029 0 NA NA NA NA307 chr1 3060001 3070000 1.7718186 0 3070000 1.7718186 T1 PRDM16308 chr1 3070001 3080000 1.5650776 0 3080000 1.5650776 T1 PRDM16................................................
Till now what I did,
p2<-ggplot(BreastCanT1T2mer, aes(start, StoZ.x)) +geom_jitter(aes(color = Hscore), pch = 23, size = 0.2) +scale_colour_manual(values = c("gray70","#525480","#9F5370","blue","red"), labels=c('NEUT', 'LOSS', 'GAIN', "DEL","AMP" ))+theme(legend.position = c(0.5, .06), legend.direction = "horizontal")+theme(legend.title = element_blank()) +geom_hline(yintercept=0, linetype="dashed", color = "black")+guides(colour = guide_legend(override.aes = list(size=1.5)))+xlab("Chromosomes") + ylab("Stoffers-Z Score")+facet_wrap(~factor(chr, c("chr1", "chr2", "chr3", "chr4", "chr5", "chr6", "chr7", "chr8", "chr9", "chr10", "chr11", "chr12", "chr13", "chr14","chr15", "chr16","chr17","chr18","chr19","chr20","chr21","chr22", "chrX", "chrY")), nrow =1, strip.position = "bottom") +theme(panel.spacing.x = unit(0.1, "lines"))+theme(axis.text.x=element_blank())+theme( legend.key = element_rect(fill = "transparent", colour = NA))p2p2+stat_peaks(span=7,size= 1, ignore_threshold = 0.95, color="brown")+stat_peaks(geom="text", size= 1.5, span=7, ignore_threshold = 0.95, color="red", angle=90, hjust=-0.1, check_overlap = TRUE) +stat_valleys(span=7,size= 1, ignore_threshold = 0.95, color="skyblue")+stat_valleys(geom="text", size= 1.5, span=7, ignore_threshold = 0.95, color="black", angle=90, hjust=1.1, check_overlap = TRUE)
My expectation is that the Gene name will appear only once where the Gene is available (StoZ is probably highest and lowest) and where the StoZ value should be less than -10 or greater than +10.
**Improvement after @Elin's sugesstion
p2+geom_text(aes(label=Gene))
Here, the Name of the Genes should appear only once and y conditioned on <-2 and >+2.
答案1
得分: 2
What I have so far is here, however, I believe the output may be better.
p2 + geom_text_repel(aes(label = ifelse(StoZ.x < -20, unique(Gene), "")), size = 1.5, angle = 45) +geom_text_repel(aes(label = ifelse(StoZ.x > 20, unique(Gene), "")), size = 1.5, angle = 45)
Now I'm wondering if I can make geom_text color based on the Tier column.
So far, what I've done hasn't yielded the desired results. Because I have called scale_color_manual in p2, I can't call it here. So I'm attempting to use scale_fill_manual, but it's not working.
p2 + geom_text_repel(aes(label = ifelse(StoZ.x < -10, unique(Gene), ""), hjust = 1, vjust = 0.5, size = 0.5, angle = 45), fill = as.factor(BreastCanT1T2mer$Tier)) +scale_fill_manual(values = c("brown", "navy"))
英文:
What I have so far is here, however, I believe the output may be better.
p2+geom_text_repel(aes(label= ifelse(StoZ.x < -20, unique(Gene), "")), size=1.5, angle = 45) +geom_text_repel(aes(label= ifelse(StoZ.x > 20, unique(Gene), "")), size=1.5, angle = 45)
Now I'm wondering if I can make geom_text color based Tier column.
So far, what I've done hasn't yielded the desired results. Because I have called scale_color_manual in p2, I can't call it here. So I'm attempting to use scale_fill_manual. but it's not working.
Hoping for advices.
p2+geom_text_repel(aes(label= ifelse(StoZ.x < -10, unique(Gene), ""), hjust = 1, vjust=.5, size=0.5, angle = 45), fill = as.factor(BreastCanT1T2mer$Tier)) +scale_fill_manual(values = c("brown", "navy"))
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