Entering edit mode
3.7 years ago
diqixiaoyaoer
▴
20
Here is my sample data and code:
## datamean_sd1<-dput(datamean_sd1[1:10,])
data<-structure(list(Organ = structure(c(1L, 1L, 1L, 1L, 2L, 2L, 2L,
2L, 2L, 2L), .Label = c("Brain\n(GSE123968)", "Brain\n(GSE95401)",
"Brain\n(E-MTAB-6910)", "Lung\nA_(GSE71159)\nC_(E-MTAB-6595)\nL_(GSE139818)\nH_(GSE137501)\nC_(GSE84345)",
"Bone\nT_(E-MTAB-6872)\nP_(E-GEOD-61636)", "Embryo\n(E-GEOD\n-69276)",
"Kidney\nD_(GSE123177)\nA_(GSE135442)", "Aorta\n(E-MTAB\n-7148)",
"Liver\nTumor_\n(E-MTAB\n-4842)\nNASH_\n(GSE119340)", "Retina\n(GSE\n144168)",
"Mus\n(GSE\n14\n15\n62)", "Lym\n(GSE\n12\n93\n15)"), class = "factor"),
Name = structure(1:10, .Label = c("1_Control", "1_Krit1",
"2_Control", "2_Pdcd20", "3_Control", "3_Acute", "3_Subacute",
"3_Chronic", "4_Control", "4_Acute", "4_Subacute", "4_Chronic",
"5_Control", "5_Acute", "5_Subacute", "5_Chronic", "6_Control_acute",
"6_Acute", "7_Control_subacute", "7_Subacute", "8_Control_chronic",
"8_Chronic", "9_Control_DG", "9_DG_VEGF", "10_Control_CA1",
"10_CA1_VEGF", "11_Control_Ectrl", "11_Control_EfCtrl", "11_E3KO",
"12_Control", "12_Cpt1_ko", "13_Control", "13_Tsc2_ko", "14_Control",
"14_Zmpste24_ko", "15_Control", "15_AM_ko", "16_Control",
"16_Chemotherapy", "16_Radiation", "16_Young", "16_Aged",
"17_EC in bone", "18_Control", "18_N1_plus_vg", "18_N1_plus_12",
"18_N1_plus_-", "18_N1_12_-", "19_Control", "19_STZ", "20_Control",
"20_AS_dimtdT", "21_Control", "21_AS_brighttdT", "22_Control",
"22_Differentiated", "23_Control", "23_Liver tumor", "24_Control",
"24_Nash", "25_Control", "25_EAU", "26_Control", "26_ iDUX4",
"27_Control", "27_RANKL_ko"), class = "factor"), Disease = structure(c(1L,
1L, 1L, 1L, 2L, 2L, 2L, 2L, 3L, 3L), .Label = c("CCM", "Seizure",
"EAE", "Stroke", "TBI", "Infla", "AOD", "CVD", "LAM", "HGPS",
"Tumor", "Pancy", "Carcino", "DK", "AS", "Home", "NASH",
"EAU", "FSHD"), class = "factor"), fill = c("#FF0000", "#FF0000",
"#00FF00", "#00FF00", "#7570B3", "#7570B3", "#7570B3", "#7570B3",
"#A6D854", "#A6D854"), mean = c(806.898912005764, 837.595854895274,
898.32650562378, 2208.81852805305, 212.969188902024, 195.692360171933,
181.622170748826, 454.592532593114, 477.034742547228, 383.52324684751
), sd = c(108.62191806741, 86.1336851228738, 108.18221445462,
551.492848636393, 35.6423740115715, 28.0730270395565, 42.7691784348475,
116.005320530673, 43.8700365938649, 63.2689449323908)), row.names = c(NA,
10L), class = "data.frame")
data
# 1
ggplot(data = data, aes(weave_factors(Name,Disease,Organ), mean,fill=fill,group=Disease))+
geom_bar(position="dodge", stat="identity",width = 0.8,color="black") +
geom_errorbar(aes(ymin = mean - sd, ymax = mean + sd),position = position_dodge(0.8), width = .2) +
theme_classic2() +
theme(legend.position = "none") +
theme(axis.text.x=element_text(vjust=1,size=10))+
labs(title = "Igfbp7", x = NULL, y = "FPKM_value") +
theme(plot.title = element_text(hjust = 0.5)) +
scale_x_discrete(guide = "axis_nested")+
theme(plot.margin = unit(c(5, 20, 30, 7), "mm"))+
# rotate_x_text(angle = 45)+
guides(x = ggh4x::guide_axis_nested(angle = -45))
Now I get this plot but I wanna draw a bigger space between different group grouping by "Disease" .
I need your help.
try faceting: https://ggplot2-book.org/facet.html
Soryy , I tried facet faceting function. You know there are three labels that should be add to x axis
Firs the common lable named Name.
Second the Disease grouping information.
The last one is Organ information which contains all of them above but stay below all of them.
And if I use faceting function I will lost the last label and I will find a other method to add it again.
You can combine disease and organ into one group (e.g. CCM_GSE12368) and facet over that.
or use ggpubr to combine plots
I'm not able to copy your example data. Can you double check it's formatted correctly?
Yeah, it works well. I promise.