COVID-19_tables_and_graphs.Rmd
Mindy Fang
2020/3/13
Load the necessary R libraries
If you haven’t installed these packages yet, please use the “install.packages” command to install them first
#install.packages("readxl")
#install.packages("dplyr")
#install.packages("ggplot2")
#install.packages("cluster")
#install.packages("table1")
#install.packages("ggpubr")
#install.packages("factoextra")
#install.packages("ggrepel")
#install.packages("ggfortify")
#install.packages("rstan")
#install.packages("boot")
#install.packages("kableExtra")
#install.packages("pscl")
library(readxl)
library(dplyr)
library(ggplot2)
library(cluster)
library(table1)
library(ggpubr)
library(factoextra)
library(ggrepel)
library(ggfortify)
library(rstan)
library(boot)
library(kableExtra)
library(pscl)Import the Tcell data
# Please change the file directory to where you have saved the "Discharged_Tcell_dat.xlsx"
Tcell_discharged = read_excel("C:/Users/mindy/Dropbox/Novel Corona Virus/Paper draft/COVID_data/Discharged_Tcell_dat.xlsx")
# Please change the file directory to where you have saved the "Death_Tcell_dat.xlsx"
Tcell_death = read_excel("C:/Users/mindy/Dropbox/Novel Corona Virus/Paper draft/COVID_data/Death_Tcell_dat.xlsx")Calculate the time intervals in days
Tcell_discharged = Tcell_discharged %>%
mutate(Dis2Hosp = as.numeric(difftime(DateofDischarge, DateofHosp,units = "days")),
Hosp2Symp = as.numeric(difftime(DateofHosp, DateofSymp, units="days")),
Dis2Symp = as.numeric(difftime(DateofDischarge, DateofSymp, units="days"))) %>%
mutate(Tcell2Symp = as.numeric(difftime(DateofTest, DateofSymp, units = "days")),
Tcell2Hosp = as.numeric(difftime(DateofTest, DateofHosp,units = "days")),
Dis2Tcell = as.numeric(difftime(DateofDischarge, DateofTest, units = "days"))) %>%
mutate(Disease=ifelse(UnderDisease=="yes",1,0))
Tcell_death = Tcell_death %>%
mutate(Death2Hosp = as.numeric(difftime(DateofDeath, DateofHosp,units = "days")),
Death2Symp = as.numeric(difftime(DateofDeath, DateofSymp, units="days")),
Hosp2Symp = as.numeric(difftime(DateofHosp, DateofSymp, units="days"))) %>%
mutate(Tcell2Symp = as.numeric(difftime(DateofTest, DateofSymp,units = "days")),
Tcell2Hosp = as.numeric(difftime(DateofTest, DateofHosp,units = "days")),
Death2Tcell = as.numeric(difftime(DateofDeath, DateofTest, units = "days")))Select the first Tcell test result after hospitalization as the baseline
Tcell_death_initial = Tcell_death %>%
group_by(PTID) %>% filter(DateofTest==min(DateofTest)) %>% mutate(Group="Death") %>%
mutate(Sex=ifelse(Gender=="M", 1, 0), Disease=ifelse(UnderDisease=="yes",1,0)) %>%
select(PTID, Group, Sex, Age, Disease, Death2Hosp, Death2Symp, Hosp2Symp,
Tcell_item1, Tcell_item2, Tcell_item3, Tcell_item4, Tcell_item5,
Tcell_item6, Tcell_item7, Tcell_item8)
Tcell_discharged_initial = Tcell_discharged %>%
group_by(PTID) %>% filter(DateofTest==min(DateofTest)) %>% mutate(Group="Discharged") %>%
mutate(Sex=ifelse(Gender=="M", 1, 0), Disease=ifelse(UnderDisease=="yes",1,0))%>%
select(PTID, Group, Sex, Age, Disease, Dis2Hosp, Dis2Symp, Hosp2Symp,
Tcell_item1, Tcell_item2, Tcell_item3, Tcell_item4, Tcell_item5,
Tcell_item6, Tcell_item7, Tcell_item8)Produce Table1
Tcell_discharged_initial$Disease = factor(Tcell_discharged_initial$Disease,
levels=c("0","1"), labels=c("No", "Yes"))
label(Tcell_discharged_initial$Disease) = "Underlying Medical Condition"
Tcell_discharged_initial$Gender = factor(Tcell_discharged_initial$Sex,
levels=c("0","1"), labels=c("Female", "Male"))
label(Tcell_discharged_initial$Dis2Hosp) = "Duration of Hospitalization"
units(Tcell_discharged_initial$Dis2Hosp) = "days"
label(Tcell_discharged_initial$Dis2Symp) = "From the First Symptom to Hospital Discharge"
units(Tcell_discharged_initial$Dis2Symp) = "days"
label(Tcell_discharged_initial$Hosp2Symp) = "From the First Symptom to Hospitalization"
units(Tcell_discharged_initial$Hosp2Symp) = "days"
table1(data=Tcell_discharged_initial, ~Age + Disease + Dis2Hosp + Hosp2Symp +
Dis2Symp|Gender, topclass = "Rtable1-zebra")| Female (n=156) |
Male (n=154) |
Overall (n=310) |
|
|---|---|---|---|
| Age | |||
| Mean (SD) | 58.8 (13.2) | 58.1 (14.7) | 58.5 (13.9) |
| Median [Min, Max] | 59.5 [21.0, 86.0] | 60.5 [22.0, 90.0] | 60.0 [21.0, 90.0] |
| Underlying Medical Condition | |||
| No | 112 (71.8%) | 90 (58.4%) | 202 (65.2%) |
| Yes | 44 (28.2%) | 64 (41.6%) | 108 (34.8%) |
| Duration of Hospitalization (days) | |||
| Mean (SD) | 12.2 (6.41) | 13.9 (8.38) | 13.0 (7.48) |
| Median [Min, Max] | 12.0 [2.00, 33.0] | 12.0 [2.00, 41.0] | 12.0 [2.00, 41.0] |
| From the First Symptom to Hospitalization (days) | |||
| Mean (SD) | 14.3 (9.30) | 14.4 (9.90) | 14.4 (9.59) |
| Median [Min, Max] | 11.0 [2.00, 43.0] | 11.0 [1.00, 57.0] | 11.0 [1.00, 57.0] |
| From the First Symptom to Hospital Discharge (days) | |||
| Mean (SD) | 26.6 (8.63) | 28.2 (11.1) | 27.4 (9.94) |
| Median [Min, Max] | 25.0 [11.0, 54.0] | 26.0 [7.00, 71.0] | 25.5 [7.00, 71.0] |
Produce Table2
Tcell_death_initial$Disease = factor(Tcell_death_initial$Disease, levels=c("0","1"),
labels=c("No", "Yes"))
label(Tcell_death_initial$Disease) = "Underlying Medical Condition"
Tcell_death_initial$Gender = factor(Tcell_death_initial$Sex, levels=c("0","1"),
labels=c("Female", "Male"))
label(Tcell_death_initial$Death2Hosp) = "Duration of Hospitalization"
units(Tcell_death_initial$Death2Hosp) = "days"
label(Tcell_death_initial$Death2Symp) = "From the First Symptom to Death"
units(Tcell_death_initial$Death2Symp) = "days"
label(Tcell_death_initial$Hosp2Symp) = "From the First Symptom to Hospitalization"
units(Tcell_death_initial$Hosp2Symp) = "days"
table1(data=Tcell_death_initial, ~Age + Disease + Death2Hosp + Hosp2Symp +
Death2Symp|Gender, topclass = "Rtable1-zebra")| Female (n=13) |
Male (n=17) |
Overall (n=30) |
|
|---|---|---|---|
| Age | |||
| Mean (SD) | 68.9 (6.42) | 69.1 (9.01) | 69.0 (7.87) |
| Median [Min, Max] | 69.0 [60.0, 85.0] | 69.0 [51.0, 81.0] | 69.0 [51.0, 85.0] |
| Underlying Medical Condition | |||
| No | 4 (30.8%) | 3 (17.6%) | 7 (23.3%) |
| Yes | 9 (69.2%) | 14 (82.4%) | 23 (76.7%) |
| Duration of Hospitalization (days) | |||
| Mean (SD) | 15.2 (9.93) | 15.0 (8.12) | 15.1 (8.78) |
| Median [Min, Max] | 12.0 [2.00, 32.0] | 13.0 [5.00, 39.0] | 12.5 [2.00, 39.0] |
| From the First Symptom to Hospitalization (days) | |||
| Mean (SD) | 13.5 (11.2) | 10.2 (4.72) | 11.7 (8.20) |
| Median [Min, Max] | 10.0 [3.00, 42.0] | 9.00 [4.00, 21.0] | 10.0 [3.00, 42.0] |
| From the First Symptom to Death (days) | |||
| Mean (SD) | 28.7 (12.2) | 25.2 (8.00) | 26.7 (10.0) |
| Median [Min, Max] | 27.0 [8.00, 53.0] | 23.0 [16.0, 48.0] | 25.5 [8.00, 53.0] |
Produce Table3
Tcell_discharged_initial$Sex = factor(Tcell_discharged_initial$Sex, levels=c("0","1"),
labels=c("Female", "Male"))
label(Tcell_discharged_initial$Tcell_item1) = "Total Lymph Cell Percentage"
units(Tcell_discharged_initial$Tcell_item1) = "%"
label(Tcell_discharged_initial$Tcell_item2) = "Total Lymph Cell Counts"
units(Tcell_discharged_initial$Tcell_item2) = "cells/ul"
label(Tcell_discharged_initial$Tcell_item3) = "Helper Lymph Cell Percentage"
units(Tcell_discharged_initial$Tcell_item3) = "%"
label(Tcell_discharged_initial$Tcell_item4) = "Helper Lymph Cell Counts"
units(Tcell_discharged_initial$Tcell_item4) = "cells/ul"
label(Tcell_discharged_initial$Tcell_item5) = "Suppressor Lymph Cell Percentage"
units(Tcell_discharged_initial$Tcell_item5) = "%"
label(Tcell_discharged_initial$Tcell_item6) = "Suppressor Lymph Cell Counts"
units(Tcell_discharged_initial$Tcell_item6) = "cells/ul"
label(Tcell_discharged_initial$Tcell_item7) = "Th/Ts(TH/TS)"
label(Tcell_discharged_initial$Tcell_item8) = "Lymph Cell Counts"
units(Tcell_discharged_initial$Tcell_item8) = "cells/ul"
table1(data=Tcell_discharged_initial, ~Tcell_item1 + Tcell_item2 + Tcell_item3 +
Tcell_item4 + Tcell_item5 + Tcell_item6 + Tcell_item7 +Tcell_item8|Sex,
topclass = "Rtable1-zebra")| Female (n=156) |
Male (n=154) |
Overall (n=310) |
|
|---|---|---|---|
| Total Lymph Cell Percentage (%) | |||
| Mean (SD) | 60.2 (11.2) | 58.1 (12.0) | 59.2 (11.6) |
| Median [Min, Max] | 62.6 [27.7, 82.4] | 58.6 [21.1, 82.7] | 61.2 [21.1, 82.7] |
| Total Lymph Cell Counts (cells/ul) | |||
| Mean (SD) | 728 (496) | 700 (508) | 714 (502) |
| Median [Min, Max] | 623 [69.6, 2070] | 656 [40.1, 2300] | 637 [40.1, 2300] |
| Helper Lymph Cell Percentage (%) | |||
| Mean (SD) | 34.7 (9.53) | 33.8 (9.93) | 34.3 (9.73) |
| Median [Min, Max] | 35.6 [14.2, 58.7] | 34.3 [6.84, 56.6] | 34.5 [6.84, 58.7] |
| Helper Lymph Cell Counts (cells/ul) | |||
| Mean (SD) | 422 (299) | 418 (329) | 420 (314) |
| Median [Min, Max] | 344 [38.0, 1410] | 340 [15.0, 1700] | 340 [15.0, 1700] |
| Suppressor Lymph Cell Percentage (%) | |||
| Mean (SD) | 25.5 (8.46) | 24.3 (8.79) | 24.9 (8.63) |
| Median [Min, Max] | 24.9 [6.80, 49.1] | 23.2 [6.75, 55.5] | 24.1 [6.75, 55.5] |
| Suppressor Lymph Cell Counts (cells/ul) | |||
| Mean (SD) | 306 (225) | 282 (210) | 294 (218) |
| Median [Min, Max] | 251 [27.0, 1120] | 244 [18.3, 1070] | 247 [18.3, 1120] |
| Th/Ts(TH/TS) | |||
| Mean (SD) | 1.57 (0.869) | 1.60 (0.785) | 1.58 (0.827) |
| Median [Min, Max] | 1.47 [0.323, 5.64] | 1.46 [0.123, 4.86] | 1.47 [0.123, 5.64] |
| Lymph Cell Counts (cells/ul) | |||
| Mean (SD) | 1150 (693) | 1160 (792) | 1160 (743) |
| Median [Min, Max] | 1010 [237, 3210] | 1010 [93.8, 4290] | 1010 [93.8, 4290] |
Produce Table4
Tcell_death_initial$Sex = factor(Tcell_death_initial$Sex, levels=c("0","1"),
labels=c("Female", "Male"))
label(Tcell_death_initial$Tcell_item1) = "Total Lymph Cell Percentage"
units(Tcell_death_initial$Tcell_item1) = "%"
label(Tcell_death_initial$Tcell_item2) = "Total Lymph Cell Counts"
units(Tcell_death_initial$Tcell_item2) = "cells/ul"
label(Tcell_death_initial$Tcell_item3) = "Helper Lymph Cell Percentage"
units(Tcell_death_initial$Tcell_item3) = "%"
label(Tcell_death_initial$Tcell_item4) = "Helper Lymph Cell Counts"
units(Tcell_death_initial$Tcell_item4) = "cells/ul"
label(Tcell_death_initial$Tcell_item5) = "Suppressor Lymph Cell Percentage"
units(Tcell_death_initial$Tcell_item5) = "%"
label(Tcell_death_initial$Tcell_item6) = "Suppressor Lymph Cell Counts"
units(Tcell_death_initial$Tcell_item6) = "cells/ul"
label(Tcell_death_initial$Tcell_item7) = "Th/Ts(TH/TS)"
label(Tcell_death_initial$Tcell_item8) = "Lymph Cell counts"
units(Tcell_death_initial$Tcell_item8) = "cells/ul"
table1(data=Tcell_death_initial, ~Tcell_item1 + Tcell_item2 + Tcell_item3 +
Tcell_item4 + Tcell_item5 + Tcell_item6 + Tcell_item7 + Tcell_item8|Sex,
topclass = "Rtable1-zebra")| Female (n=13) |
Male (n=17) |
Overall (n=30) |
|
|---|---|---|---|
| Total Lymph Cell Percentage (%) | |||
| Mean (SD) | 50.9 (14.1) | 52.1 (14.2) | 51.6 (14.0) |
| Median [Min, Max] | 47.9 [26.6, 75.4] | 53.4 [18.5, 72.0] | 51.7 [18.5, 75.4] |
| Total Lymph Cell Counts (cells/ul) | |||
| Mean (SD) | 240 (129) | 206 (184) | 221 (161) |
| Median [Min, Max] | 212 [78.0, 456] | 110 [35.8, 719] | 170 [35.8, 719] |
| Helper Lymph Cell Percentage (%) | |||
| Mean (SD) | 34.4 (13.3) | 34.7 (11.5) | 34.6 (12.1) |
| Median [Min, Max] | 38.0 [13.9, 51.6] | 36.6 [13.9, 52.0] | 37.3 [13.9, 52.0] |
| Helper Lymph Cell Counts (cells/ul) | |||
| Mean (SD) | 165 (113) | 123 (88.0) | 141 (99.9) |
| Median [Min, Max] | 129 [53.9, 385] | 77.8 [24.5, 322] | 117 [24.5, 385] |
| Suppressor Lymph Cell Percentage (%) | |||
| Mean (SD) | 16.5 (6.58) | 17.3 (10.0) | 17.0 (8.56) |
| Median [Min, Max] | 19.0 [7.42, 27.2] | 15.2 [4.55, 47.6] | 16.0 [4.55, 47.6] |
| Suppressor Lymph Cell Counts (cells/ul) | |||
| Mean (SD) | 75.2 (47.9) | 82.4 (122) | 79.3 (95.7) |
| Median [Min, Max] | 70.8 [21.8, 211] | 44.6 [11.3, 512] | 55.7 [11.3, 512] |
| Th/Ts(TH/TS) | |||
| Mean (SD) | 2.50 (1.42) | 2.51 (1.31) | 2.51 (1.34) |
| Median [Min, Max] | 2.26 [0.510, 5.45] | 2.42 [0.403, 5.88] | 2.34 [0.403, 5.88] |
| Lymph Cell counts (cells/ul) | |||
| Mean (SD) | 474 (232) | 385 (269) | 424 (253) |
| Median [Min, Max] | 381 [126, 951] | 304 [67.0, 1080] | 374 [67.0, 1080] |
Combine Data and scale the selected subset of the data into standardized normal distribution Normal(0,1)
Initial_combined = rbind(subset(Tcell_discharged_initial,select = -c(Dis2Hosp,Dis2Symp)),
subset(Tcell_death_initial, select = -c(Death2Hosp,Death2Symp)))
Tcell_3ind = Initial_combined[,c("Age", "Disease", "Tcell_item4","Tcell_item6","Tcell_item7","Tcell_item2","Group")]
colnames(Tcell_3ind) = c("Age", "Disease", "Helper_Lymph_Cell",
"Suppressor_Lymph_Cell", "TH_TS_ratio","Total_Lymph_Cell", "Group")
Tcell_3ind_scaled = Tcell_3ind
Tcell_3ind_scaled$Disease = ifelse(Tcell_3ind_scaled$Disease == "Yes",1,0)
Tcell_3ind_scaled = as.data.frame(scale(Tcell_3ind_scaled[,-c(6:7)]))
colnames(Tcell_3ind_scaled) = c("Age", "Disease", "Helper_Lymph_Cell",
"Suppressor_Lymph_Cell", "TH_TS_ratio") Produce Figure2
Tcell_discharged_initial %>%
select(Age, Disease, Dis2Hosp) %>%
ggplot(aes(x=Age, y=Dis2Hosp, color=Disease)) +
geom_point()+ theme_minimal()+ theme(legend.title=element_blank())+
scale_color_manual(values=c("lightpink", "royalblue"))+
geom_smooth(method='lm', formula= y~x)+ylab("Duration of Hospitalization")
Tcell_death_initial %>%
select(Age, Disease, Death2Hosp) %>%
ggplot(aes(x=Age, y=Death2Hosp, color=Disease)) +
geom_point()+ theme_minimal()+ theme(legend.title=element_blank())+
scale_color_manual(values=c("lightpink", "royalblue"))+
geom_smooth(method='lm', formula= y~x)+ylab("Duration of Hospitalization")
Produce Figure3
ggboxplot(data=Initial_combined, y="Tcell_item2", x="Group", fill="Group") +
stat_compare_means(method = "t.test") +
geom_boxplot(alpha=0.4,color="lightgrey") +
scale_fill_manual(name="Group", labels=c("Death","Discharged"),
breaks = c("Death","Discharged"),
values=c("lightcoral", "mediumseagreen")) +
theme_minimal() + xlab("") + ylab("") + theme(legend.position = "none")
ggboxplot(data=Initial_combined, y="Tcell_item4", x="Group", fill="Group") +
stat_compare_means(method = "t.test") +
geom_boxplot(alpha=0.4,color="lightgrey") +
scale_fill_manual(name="Group", labels=c("Death","Discharged"),
breaks = c("Death","Discharged"),
values=c("lightcoral", "mediumseagreen")) +
theme_minimal()+xlab("")+ylab("") + theme(legend.position = "none")
ggboxplot(data=Initial_combined, y="Tcell_item6", x="Group", fill="Group") +
stat_compare_means(method = "t.test") +
geom_boxplot(alpha=0.4,color="lightgrey") +
scale_fill_manual(name="Group", labels=c("Death","Discharged"),
breaks = c("Death","Discharged"),
values=c("lightcoral", "mediumseagreen")) +
theme_minimal()+xlab("")+ylab("") + theme(legend.position = "none")
ggboxplot(data=Initial_combined, y="Tcell_item7", x="Group", fill="Group") +
stat_compare_means(method = "t.test") +
geom_boxplot(alpha=0.4,color="lightgrey") +
scale_fill_manual(name="Group", labels=c("Death","Discharged"),
breaks = c("Death","Discharged"),
values=c("lightcoral", "mediumseagreen")) +
theme_minimal()+xlab("")+ylab("") + theme(legend.position = "none")
Produce Figure4
Tcell_3ind %>%
ggplot(aes(y=Helper_Lymph_Cell, x=Total_Lymph_Cell, color = factor(Group), label = Group)) +
geom_point()+ theme_minimal()+ theme(legend.title=element_blank())+
scale_color_manual(values=c("lightcoral", "mediumseagreen"))
Tcell_3ind %>%
ggplot(aes(y=Suppressor_Lymph_Cell, x=Total_Lymph_Cell, color = factor(Group), label = Group)) +
geom_point()+ theme_minimal()+ theme(legend.title=element_blank())+
scale_color_manual(values=c("lightcoral", "mediumseagreen"))
Tcell_3ind %>%
ggplot(aes(y=Suppressor_Lymph_Cell, x=Helper_Lymph_Cell, color = factor(Group), label = Group)) +
geom_point()+ theme_minimal()+ theme(legend.title=element_blank())+
scale_color_manual(values=c("lightcoral", "mediumseagreen"))
Produce Figure5 a)
Tcell_pca = clara(Tcell_3ind_scaled, 2)
autoplot(Tcell_pca,loadings=TRUE, loadings.label = TRUE,
loadings.label.colour = "lightblue4", loadings.label.size = 5,
loadings.colour = "lightblue4") +
scale_color_manual(name="", labels=c("",""), breaks = c("1", "2"),
values=c("peachpuff", "peachpuff")) +
theme(legend.text = element_text(size = 16)) + theme_minimal()
Produce Figure5 b)
fviz_cluster(list(data = Tcell_3ind_scaled,
cluster=as.factor(Initial_combined$Group)), geom="point") +
scale_fill_manual(values=c("lightcoral", "mediumseagreen")) +
theme_minimal()+xlab("")+ylab("")+ggtitle("")+theme(legend.title = element_blank())
save(Tcell_3ind,file="C:/Users/mindy/Dropbox/Novel Corona Virus/Paper draft/COVID_data/WebApp.RData")