R绘制棒棒图和通路展示

R绘制棒棒图并且合并富集的结果

图像可视化


celltyep_barplot_basic_pathway.png

分析文件如下：

cat gene_number.xls
cell_marker_number      celltype
4986    B_cell
2586    Cd4_Tcell
2959    Cd8_Tcell
1016    Erythrocytes
761     Macrophage
1470    Monocytes
2563    Neutrophil
2148    NK_cell
362     Plasma_cells
1225    pro-B_cells
2282    Proliferating_cell

cat new_pathway.xls
celltype        Category        ID      Description     GeneRatio       BgRatio pvalue  padj    geneID  geneName        Count
B_cell  BP      GO:0030888      regulation of B cell proliferation      27/4334 60/20662        2.5226793904278e-05     0.000529498055270563    ENSMUSG00000104213/ENSMUSG00000024610/ENSMUSG00000005583/ENSMUSG00000068105/ENSMUSG00000024353/ENSMUSG00000030468/ENSMUSG00000010142/ENSMUSG00000017652/ENSMUSG00000018168/ENSMUSG00000029084/ENSMUSG00000031264/ENSMUSG00000051212/ENSMUSG00000037706/ENSMUSG00000020167/ENSMUSG00000042228/ENSMUSG00000036526/ENSMUSG00000026288/ENSMUSG00000026739/ENSMUSG00000047139/ENSMUSG00000033307/ENSMUSG00000038894/ENSMUSG00000034218/ENSMUSG00000040663/ENSMUSG00000025986/ENSMUSG00000047123/ENSMUSG00000045322/ENSMUSG00000031101Ighd/Cd74/Mef2c/Tnfrsf13c/Mzb1/Siglecg/Tnfrsf13b/Cd40/Ikzf3/Cd38/Btk/Gpr183/Cd81/Tcf3/Lyn/Card11/Inpp5d/Bmi1/Cd24a/Mif/Irs2/Atm/Clcf1/Slc39a10/Ticam1/Tlr9/Sash3   27
Cd4_Tcell       BP      GO:0035710      CD4-positive, alpha-beta T cell activation      28/2294 92/20662        4.09501431465164e-07    2.93292915487184e-05    ENSMUSG00000027985/ENSMUSG00000026778/ENSMUSG00000051457/ENSMUSG00000023927/ENSMUSG00000015619/ENSMUSG00000032238/ENSMUSG00000025880/ENSMUSG00000039521/ENSMUSG00000026070/ENSMUSG00000038037/ENSMUSG00000037944/ENSMUSG00000020101/ENSMUSG00000034266/ENSMUSG00000039942/ENSMUSG00000031304/ENSMUSG00000029053/ENSMUSG00000028042/ENSMUSG00000000869/ENSMUSG00000028150/ENSMUSG00000049103/ENSMUSG00000004040/ENSMUSG00000040423/ENSMUSG00000027720/ENSMUSG00000031101/ENSMUSG00000030748/ENSMUSG00000031885/ENSMUSG00000075376/ENSMUSG00000015314     Lef1/Prkcq/Spn/Satb1/Gata3/Rora/Smad7/Foxp3/Il18r1/Socs1/Ccr7/Vsir/Batf/Ptger4/Il2rg/Prkcz/Zbtb7b/Il4/Rorc/Ccr2/Stat3/Rc3h1/Il2/Sash3/Il4ra/Cbfb/Rc3h2/Slamf6       28
Cd8_Tcell       BP      GO:0036037      CD8-positive, alpha-beta T cell activation      11/2670 25/20662        0.000128069583625087    0.00237802855435915     ENSMUSG00000023927/ENSMUSG00000070691/ENSMUSG00000027843/ENSMUSG00000028362/ENSMUSG00000032446/ENSMUSG00000020101/ENSMUSG00000057329/ENSMUSG00000038037/ENSMUSG00000018899/ENSMUSG00000026573/ENSMUSG00000031885        Satb1/Runx3/Ptpn22/Tnfsf8/Eomes/Vsir/Bcl2/Socs1/Irf1/Xcl1/Cbfb  11
Erythrocytes    BP      GO:0048821      erythrocyte development 10/979  36/20662        4.48887773698108e-06    7.94960443346979e-05    ENSMUSG00000031162/ENSMUSG00000028717/ENSMUSG00000031543/ENSMUSG00000023926/ENSMUSG00000069919/ENSMUSG00000067367/ENSMUSG00000069917/ENSMUSG00000051910/ENSMUSG00000006574/ENSMUSG00000022099  Gata1/Tal1/Ank1/Rhag/Hba-a1/Lyar/Hba-a2/Sox6/Slc4a1/Dmtn 10
Macrophage      BP      GO:1905517      macrophage migration    5/699   51/20662        0.0285235351794117      0.102655330342562       ENSMUSG00000037706/ENSMUSG00000050335/ENSMUSG00000022667/ENSMUSG00000029470/ENSMUSG00000042190      Cd81/Lgals3/Cd200r1/P2rx4/Cmklr1        5
Monocytes       BP      GO:0002548      monocyte chemotaxis     11/1351 60/20662        0.00157993978331529     0.0155683958070725      ENSMUSG00000024397/ENSMUSG00000022892/ENSMUSG00000050335/ENSMUSG00000035042/ENSMUSG00000030223/ENSMUSG00000061778/ENSMUSG00000031779/ENSMUSG00000041120/ENSMUSG00000021190/ENSMUSG00000049103/ENSMUSG00000028466        Aif1/App/Lgals3/Ccl5/Ptpro/Mospd2/Ccl22/Nbl1/Lgmn/Ccr2/Creb3    11
Neutrophil      BP      GO:1990266      neutrophil migration    48/2230 116/20662       1.59564980363204e-17    2.06636649570349e-15    ENSMUSG00000056071/ENSMUSG00000056054/ENSMUSG00000027398/ENSMUSG00000028859/ENSMUSG00000058715/ENSMUSG00000026180/ENSMUSG00000018927/ENSMUSG00000049130/ENSMUSG00000050335/ENSMUSG00000041754/ENSMUSG00000048534/ENSMUSG00000073982/ENSMUSG00000029082/ENSMUSG00000032508/ENSMUSG00000001847/ENSMUSG00000052212/ENSMUSG00000042265/ENSMUSG00000026981/ENSMUSG00000025473/ENSMUSG00000026581/ENSMUSG00000033220/ENSMUSG00000031402/ENSMUSG00000039621/ENSMUSG00000059883/ENSMUSG00000019122/ENSMUSG00000055994/ENSMUSG00000058427/ENSMUSG00000000982/ENSMUSG00000018930/ENSMUSG00000016024/ENSMUSG00000054400/ENSMUSG00000033721/ENSMUSG00000005103/ENSMUSG00000057729/ENSMUSG00000034855/ENSMUSG00000074361/ENSMUSG00000042284/ENSMUSG00000039145/ENSMUSG00000021457/ENSMUSG00000048480/ENSMUSG00000029373/ENSMUSG00000021699/ENSMUSG00000034116/ENSMUSG00000029372/ENSMUSG00000004814/ENSMUSG00000031616/ENSMUSG00000029304/ENSMUSG00000022488 S100a9/S100a8/Il1b/Csf3r/Fcer1g/Cxcr2/Ccl6/C5ar1/Lgals3/Trem3/Jaml/Rhog/Bst1/Myd88/Rac1/Cd177/Trem1/Il1rn/Adam8/Sell/Rac2/Mpp1/Prex1/Irak4/Ccl9/Nod2/Cxcl2/Ccl3/Ccl4/Lbp/Cklf/Vav3/Wdr1/Prtn3/Cxcl10/C5ar2/Itga1/Camk1d/Syk/Cxcr1/Pf4/Pde4d/Vav1/Ppbp/Ccl24/Ednra/Spp1/Nckap1l  48
NK_cell BP      GO:0002228      natural killer cell mediated immunity   19/1975 58/20662        9.54025401078115e-07    4.38927400797606e-05    ENSMUSG00000030165/ENSMUSG00000030149/ENSMUSG00000050241/ENSMUSG00000026068/ENSMUSG00000005696/ENSMUSG00000039315/ENSMUSG00000045827/ENSMUSG00000034028/ENSMUSG00000038304/ENSMUSG00000060216/ENSMUSG00000022657/ENSMUSG00000079298/ENSMUSG00000057948/ENSMUSG00000032021/ENSMUSG00000032202/ENSMUSG00000024339/ENSMUSG00000079685/ENSMUSG00000030124/ENSMUSG00000051412    Klrd1/Klrk1/Klre1/Il18rap/Sh2d1a/Clnk/Serpinb9/Cd226/Cd160/Arrb2/Cd96/Klrb1b/Unc13d/Crtam/Rab27a/Tap2/Ulbp1/Lag3/Vamp7  19
Plasma_cells    BP      GO:0006959      humoral immune response 10/328  347/20662       0.0512446845531989      0.482835396074602       ENSMUSG00000067149/ENSMUSG00000017002/ENSMUSG00000076617/ENSMUSG00000022018/ENSMUSG00000105906/ENSMUSG00000076937/ENSMUSG00000037706/ENSMUSG00000060802/ENSMUSG00000095079/ENSMUSG00000096459  Jchain/Slpi/Ighm/Rgcc/Iglc1/Iglc2/Cd81/B2m/Igha/Ighv9-3  10
pro-B_cells     MF      GO:0003823      antigen binding 8/1124  175/20558       0.746799320773681       0.904294708255282       ENSMUSG00000015355/ENSMUSG00000002603/ENSMUSG00000037321/ENSMUSG00000073409/ENSMUSG00000016206/ENSMUSG00000024339/ENSMUSG00000035929/ENSMUSG00000059208     Cd48/Tgfb1/Tap1/H2-Q6/H2-M3/Tap2/H2-Q4/Hnrnpm       8
Proliferating_cell      BP      GO:0031349      positive regulation of defense response 28/2189 348/20662       0.954490161531633       0.999999999948877       ENSMUSG00000054717/ENSMUSG00000066551/ENSMUSG00000033307/ENSMUSG00000028820/ENSMUSG00000025980/ENSMUSG00000047139/ENSMUSG00000031311/ENSMUSG00000015217/ENSMUSG00000018446/ENSMUSG00000079685/ENSMUSG00000001666/ENSMUSG00000057135/ENSMUSG00000028964/ENSMUSG00000030793/ENSMUSG00000002944/ENSMUSG00000031948/ENSMUSG00000022901/ENSMUSG00000040952/ENSMUSG00000037706/ENSMUSG00000039316/ENSMUSG00000051412/ENSMUSG00000022471/ENSMUSG00000006456/ENSMUSG00000026672/ENSMUSG00000005312/ENSMUSG00000028099/ENSMUSG00000029203/ENSMUSG00000042419     Hmgb2/Hmgb1/Mif/Sfpq/Hspd1/Cd24a/Nono/Hmgb3/C1qbp/Ulbp1/Ddt/Scimp/Park7/Pycard/Cd36/Kars/Cd86/Rps19/Cd81/Rftn1/Vamp7/Xrcc6/Rbm14/Optn/Ubqln1/Polr3c/Ube2k/Nfkbil1   28

绘制代码如下：

# 加载包
library(ggplot2)
library(tidyverse)
rm(list=ls())
# 读取细胞marker基因数的数据
data <- read.table("gene_number.xls",sep="\t",header=T)
data <-data %>% mutate(celltype = factor(celltype, levels = rev(celltype)))
# 绘制棒棒图
p1<-ggplot(data, aes(cell_marker_number, celltype, color = celltype)) +
  geom_segment(aes(yend =celltype ), color = "grey", xend = 0) +
  geom_point(aes(size = cell_marker_number), show.legend = FALSE) +
  guides(colour = guide_legend(override.aes = list(shape = 15, size = 6))) +
  scale_size_area(max_size = 10) +labs(title  = "Cell marker numbers", y = " ",x=" ")+
  scale_color_manual(values = c("B_cell"="#DD2233","Cd4_Tcell"="#8169A9","Cd8_Tcell"="#88554C","Erythrocytes"="#F27F33","Macrophage"="#299948","Monocytes"="#ABB532","Neutrophil"="#06B3C5","NK_cell"="#0B74B2","Plasma_cells"="#D278AF","pro-B_cells"="#13A699","Proliferating_cell"="#BC3E03")) +
  theme_bw() +
  theme(panel.background = element_blank(),
    panel.grid= element_blank(),
    axis.text.x = element_text(color="black",angle = 0, size = 12, hjust = 1),
    axis.text.y = element_text(size = 12,color="black"),
    legend.title = element_text(size = 15),
    legend.key.height = unit(0.8, "cm"),
    legend.text = element_text(size = 12),
    strip.text = element_text(size = 15),
    legend.justification = "top",
    plot.title = element_text(hjust = 0.5))

#读取通路文件
path<-read.table("new_pathway.xls",sep="\t",header=T)
path <-path %>% mutate(celltype = factor(celltype, levels = rev(celltype)))

p2<-ggplot(path,aes(x=-log10(pvalue),y=celltype,fill=celltype))+geom_bar(stat='identity')+
geom_text(aes(label = Description ), hjust =0.8,size = 3)+labs(title="GO enrichment item",y=" ")+
  scale_fill_manual(values = c("B_cell"="#DD2233","Cd4_Tcell"="#8169A9","Cd8_Tcell"="#88554C","Erythrocytes"="#F27F33","Macrophage"="#299948","Monocytes"="#ABB532","Neutrophil"="#06B3C5","NK_cell"="#0B74B2","Plasma_cells"="#D278AF","pro-B_cells"="#13A699","Proliferating_cell"="#BC3E03"
                               ))+theme_bw()+
  theme(panel.background = element_blank(),panel.grid= element_blank(),axis.text.x = element_text(color="black",angle = 0, size = 12, hjust = 1),
        plot.title = element_text(hjust = 0.5),axis.text.y = element_blank(),axis.ticks.y = element_blank(),legend.position = "none")
p2

library(patchwork)
p3<-p1 + p2

# 保存图像
ggsave("celltyep_barplot_basic_pathway.png", p3, width = 8, height = 6, dpi = 600)
ggsave("celltyep_barplot_basic_pathway.pdf", p3, width = 8, height = 6, dpi = 600)
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