数据帧熔解问题与气泡图

Question

这是我的数据

a <- dput(df)
structure(list(Category = c("KEGG Pathway", "KEGG Pathway", "KEGG Pathway", 
"KEGG Pathway", "KEGG Pathway", "KEGG Pathway", "KEGG Pathway", 
"KEGG Pathway", "KEGG Pathway", "KEGG Pathway", "KEGG Pathway", 
"KEGG Pathway", "KEGG Pathway", "KEGG Pathway", "KEGG Pathway", 
"KEGG Pathway", "Reactome Gene Sets", "Reactome Gene Sets", "Reactome Gene Sets", 
"Reactome Gene Sets", "Reactome Gene Sets", "Reactome Gene Sets", 
"Reactome Gene Sets", "Reactome Gene Sets", "Reactome Gene Sets", 
"Reactome Gene Sets", "Reactome Gene Sets"), Description = c("Cytokine-cytokine receptor interaction", 
"Cytokine-cytokine receptor interaction", "Salmonella infection", 
"Rheumatoid arthritis", "Salmonella infection", "Rheumatoid arthritis", 
"Toll-like receptor signaling pathway", "Toll-like receptor signaling pathway", 
"Chemokine signaling pathway", "Chemokine signaling pathway", 
"PI3K-Akt signaling pathway", "PI3K-Akt signaling pathway", "Rap1 signaling pathway", 
"Rap1 signaling pathway", "TNF signaling pathway", "TNF signaling pathway", 
"Interleukin-10 signaling", "Cytokine Signaling in Immune system", 
"Chemokine receptors bind chemokines", "Signaling by GPCR", "Signaling by Interleukins", 
"Peptide ligand-binding receptors", "GPCR ligand binding", "GPCR downstream signalling", 
"Class A/1 (Rhodopsin-like receptors)", "Signaling by Receptor Tyrosine Kinases", 
"Metabolism of nucleotides"), LogP = c(-6.6272284368, -6.6272284368, 
-2.9316614282, -2.8584315312, -2.7718494704, -2.7061868255, -2.6281915791, 
-2.6281915791, -2.5273777647, -2.5273777647, -3.6762135505, -3.2880356369, 
-2.2646576514, -2.117278626, -3.5410827773, -3.4151337331, -8.2548924333, 
-6.5328526991, -4.7978866035, -3.9736787567, -3.7112985062, -3.1255339841, 
-3.0317801957, -2.6859542446, -2.6603292838, -3.2998550411, -2.690237169
)), row.names = c(NA, -27L), class = c("data.table", "data.frame"
), .internal.selfref = <pointer: 0x5642e14a3420>)

这是这样的

head(a)
       Category                            Description      LogP
1: KEGG Pathway Cytokine-cytokine receptor interaction -6.627228
2: KEGG Pathway Cytokine-cytokine receptor interaction -6.627228
3: KEGG Pathway                   Salmonella infection -2.931661
4: KEGG Pathway                   Rheumatoid arthritis -2.858432
5: KEGG Pathway                   Salmonella infection -2.771849
6: KEGG Pathway                   Rheumatoid arthritis -2.706187

在这个类别列中，我有两个独特的组，KEGG和Reactome。

所以我试着用这样的长格式融化

pcm = melt(df, id = c("Description"))

pcm$Description <- factor(pcm$Description,levels=unique(pcm$Description))

colours = c( "#A54657",  "#582630", "#F7EE7F", "#4DAA57","#F1A66A","#F26157", "#F9ECCC", "#679289", "#33658A",
             "#F6AE2D","#86BBD8")


xx = ggplot(pcm, aes(x = variable, y = Description)) + 
  geom_point(aes(size = value, fill = variable), alpha = 0.75, shape = 21) + 
  #scale_size_continuous(limits = c(-6, -1), range = c(1,17), breaks = c(1,10,50,75)) + 
  labs( x= "", y = "", size = "p value (%)", fill = "")  + 
  theme(legend.key=element_blank(), 
        axis.text.x = element_text(colour = "black", size = 12, face = "bold", angle = 90, vjust = 0.3, hjust = 1), 
        axis.text.y = element_text(colour = "black", face = "bold", size = 11), 
        legend.text = element_text(size = 10, face ="bold", colour ="black"), 
        legend.title = element_text(size = 12, face = "bold"), 
        panel.background = element_blank(), panel.border = element_rect(colour = "black", fill = NA, size = 1.2), 
        legend.position = "right") +  
  scale_fill_manual(values = colours, guide = FALSE) + 
  scale_y_discrete(limits = rev(levels(pcm$Description))) 

xx

​

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但这个我搞砸了

我需要的是在我的x轴，我只想要我的两个类别和我的y轴描述标签，我不确定，如果两个传奇的pvalue可以进去。

如有任何建议或帮助，将不胜感激。

更新

d <- unique_GO %>% group_by(Category) %>% slice_min(order_by = LogP, n = 10)




df$Description <- factor(d$Description,levels=unique(df$Description))

colours = c( "#A54657",  "#582630", "#F7EE7F", "#4DAA57","#F1A66A","#F26157", "#F9ECCC", "#679289", "#33658A",
             "#F6AE2D","#86BBD8")

ggplot(df, aes(x = Category, y = Description)) + 
  geom_point(aes(size = LogP, fill = Category), alpha = 0.75, shape = 21) + 
scale_y_discrete(limits = rev(levels(df$Description))) 

​

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Answer 1

您的数据在a中已经是长格式的，ggplot可以很好地处理。

a$Description <- factor(a$Description,levels=unique(a$Description))

colours = c( "#A54657",  "#582630", "#F7EE7F", "#4DAA57","#F1A66A","#F26157", "#F9ECCC", "#679289", "#33658A",
             "#F6AE2D","#86BBD8")

ggplot(a, aes(x = Category, y = Description)) + 
   geom_point(aes(size = LogP, fill = Category), alpha = 0.75, shape = 21) + 
   ...
   scale_y_discrete(limits = rev(levels(a$Description))) 

​

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编辑

有很多方法来摆弄文字间距。这里有一种使用空白的方法：

library(ggplot2); library(dplyr)
ggplot(a, aes(x = Category, y = Description)) + 
   geom_point(aes(size = LogP, fill = Category), alpha = 0.75, shape = 21) + 
   #scale_size_continuous(limits = c(-6, -1), range = c(1,17), breaks = c(1,10,50,75)) + 
   geom_text(data = a %>% filter(Category != "KEGG Pathway"),
             aes(label = Description), hjust = 1, nudge_x = -0.1) +
   geom_text(data = a %>% filter(Category == "KEGG Pathway"),
             aes(label = Description), hjust = 0, nudge_x = 0.1) +
   coord_cartesian(clip = "off") +
   
   labs( x= "", y = "", size = "p value (%)", fill = "")  + 
   theme(legend.key=element_blank(), 
         
         axis.text.x = element_text(colour = "black", size = 12, face = "bold", angle = 90, vjust = 0.3, hjust = 1), 
         axis.text.y = element_blank(),
         legend.text = element_text(size = 10, face ="bold", colour ="black"), 
         legend.title = element_text(size = 12, face = "bold"), 
         panel.background = element_blank(), panel.border = element_rect(colour = "black", fill = NA, size = 1.2), 
         legend.position = "right") +  
   scale_fill_manual(values = colours, guide = FALSE) + 
   scale_y_discrete(limits = rev(levels(a$Description)))

​

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