R Notebook

rr

View(tumorgrowth)
View(Avg_volume_tumor_kinetics)
library(\ggplot2\)
library(ggfortify)
library(survival)

View(tumorgrowth)
ggplot(tumorgrowth, aes(x = (Day), y = Volume, colour = Tx)) + 
  geom_point() + xlab('Day') +
  geom_line()+
  theme_bw()

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View(Avg_volume_tumor_kinetics)
ggplot(Avg_volume_tumor_kinetics, aes(x = (Day), y = AvgVolume, colour = Tx)) + 
  geom_point() + xlab('Day') +
  geom_line()+
  theme_bw()

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library(\ggplot2\)
library(ggfortify)
library(survival)

View(survival)
#with confidence interval
fit <- survfit(Surv(time, event) ~ Group, data = survival)
autoplot(fit)

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#no confidence interval 
autoplot(fit, surv.linetype = 'dashed', conf.int = FALSE,
         censor.shape = \*\, censor.size = 5, facets = TRUE, ncol = 2)

Using formula(x) is deprecated when x is a character vector of length > 1.
  Consider formula(paste(x, collapse = \ \)) instead.

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#all 4 on 1 plot 
fit <- survfit(Surv(time, event) ~ Group, data = survival)
autoplot(fit)

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autoplot(fit, surv.linetype = 'dashed', conf.int = FALSE)

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res.aov <- aov(time ~ Group, data = survival)
TukeyHSD(res.aov)

  Tukey multiple comparisons of means
    95% family-wise confidence level

Fit: aov(formula = time ~ Group, data = survival)

$Group
               diff       lwr       upr     p adj
Ctrl-4PF -29.887500 -60.88312  1.108123 0.0628348
PF-4PF   -35.401786 -68.62742 -2.176150 0.0322640
XPF-4PF  -18.270833 -56.50666 19.964993 0.5938166
PF-Ctrl   -5.514286 -34.00195 22.973382 0.9567983
XPF-Ctrl  11.616667 -22.58250 45.815829 0.8087367
XPF-PF    17.130952 -19.10159 53.363492 0.6021598

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summary(res.aov)

            Df Sum Sq Mean Sq F value Pr(>F)  
Group        3  13363    4454   3.068  0.033 *
Residuals   75 108901    1452                 
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

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summary(survival)

    mouseID        Group                time           event       
 Min.   : 1.0   Length:79          Min.   : 87.0   Min.   :0.0000  
 1st Qu.:20.5   Class :character   1st Qu.:137.5   1st Qu.:1.0000  
 Median :40.0   Mode  :character   Median :174.0   Median :1.0000  
 Mean   :40.0                      Mean   :169.2   Mean   :0.9873  
 3rd Qu.:59.5                      3rd Qu.:197.5   3rd Qu.:1.0000  
 Max.   :79.0                      Max.   :249.0   Max.   :1.0000  

res.aov <- aov(AvgVolume ~ Tx, data = Avg_volume_tumor_kinetics)
TukeyHSD(res.aov)

  Tukey multiple comparisons of means
    95% family-wise confidence level

Fit: aov(formula = AvgVolume ~ Tx, data = Avg_volume_tumor_kinetics)

$Tx
              diff       lwr      upr     p adj
Ctrl-4PF 149.94000 -280.3309 580.2109 0.6536861
PF-4PF   181.36214 -248.9088 611.6331 0.5406753
PF-Ctrl   31.42214 -398.8488 461.6931 0.9810517

summary(res.aov)

            Df  Sum Sq Mean Sq F value Pr(>F)
Tx           2  131510   65755   0.661  0.528
Residuals   18 1790638   99480               

res.aov <- aov(Volume ~ Tx, data = tumorgrowth)
TukeyHSD(res.aov)

  Tukey multiple comparisons of means
    95% family-wise confidence level

Fit: aov(formula = Volume ~ Tx, data = tumorgrowth)

$Tx
                   diff         lwr       upr     p adj
4PF12-4PF11  151.457143  -480.10198  783.0163 0.9999406
4PF13-4PF11  161.400000  -470.15912  792.9591 0.9998737
4PF14-4PF11  254.414286  -377.14484  885.9734 0.9847141
4PF15-4PF11  331.571429  -299.98769  963.1306 0.8782914
Ctrl1-4PF11  597.671429   -33.88769 1229.2306 0.0833143
Ctrl2-4PF11  251.728571  -379.83055  883.2877 0.9861157
Ctrl3-4PF11  286.000000  -345.55912  917.5591 0.9585589
Ctrl4-4PF11  145.314286  -486.24484  776.8734 0.9999640
Ctrl5-4PF11  367.828571  -263.73055  999.3877 0.7734955
PF10-4PF11    29.614286  -662.22407  721.4526 1.0000000
PF6-4PF11    508.928571  -122.63055 1140.4877 0.2601162
PF7-4PF11    614.085714   -17.47341 1245.6448 0.0653695
PF8-4PF11    342.900000  -288.65912  974.4591 0.8492843
PF9-4PF11     86.400000  -545.15912  717.9591 1.0000000
4PF13-4PF12    9.942857  -621.61627  641.5020 1.0000000
4PF14-4PF12  102.957143  -528.60198  734.5163 0.9999995
4PF15-4PF12  180.114286  -451.44484  811.6734 0.9995533
Ctrl1-4PF12  446.214286  -185.34484 1077.7734 0.4752203
Ctrl2-4PF12  100.271429  -531.28769  731.8306 0.9999997
Ctrl3-4PF12  134.542857  -497.01627  766.1020 0.9999860
Ctrl4-4PF12   -6.142857  -637.70198  625.4163 1.0000000
Ctrl5-4PF12  216.371429  -415.18769  847.9306 0.9967889
PF10-4PF12  -121.842857  -813.68121  569.9955 0.9999987
PF6-4PF12    357.471429  -274.08769  989.0306 0.8068548
PF7-4PF12    462.628571  -168.93055 1094.1877 0.4131325
PF8-4PF12    191.442857  -440.11627  823.0020 0.9991209
PF9-4PF12    -65.057143  -696.61627  566.5020 1.0000000
4PF14-4PF13   93.014286  -538.54484  724.5734 0.9999999
4PF15-4PF13  170.171429  -461.38769  801.7306 0.9997661
Ctrl1-4PF13  436.271429  -195.28769 1067.8306 0.5140167
Ctrl2-4PF13   90.328571  -541.23055  721.8877 0.9999999
Ctrl3-4PF13  124.600000  -506.95912  756.1591 0.9999946
Ctrl4-4PF13  -16.085714  -647.64484  615.4734 1.0000000
Ctrl5-4PF13  206.428571  -425.13055  837.9877 0.9980272
PF10-4PF13  -131.785714  -823.62407  560.0526 0.9999966
PF6-4PF13    347.528571  -284.03055  979.0877 0.8364117
PF7-4PF13    452.685714  -178.87341 1084.2448 0.4503945
PF8-4PF13    181.500000  -450.05912  813.0591 0.9995131
PF9-4PF13    -75.000000  -706.55912  556.5591 1.0000000
4PF15-4PF14   77.157143  -554.40198  708.7163 1.0000000
Ctrl1-4PF14  343.257143  -288.30198  974.8163 0.8483118
Ctrl2-4PF14   -2.685714  -634.24484  628.8734 1.0000000
Ctrl3-4PF14   31.585714  -599.97341  663.1448 1.0000000
Ctrl4-4PF14 -109.100000  -740.65912  522.4591 0.9999990
Ctrl5-4PF14  113.414286  -518.14484  744.9734 0.9999984
PF10-4PF14  -224.800000  -916.63836  467.0384 0.9981460
PF6-4PF14    254.514286  -377.04484  886.0734 0.9846598
PF7-4PF14    359.671429  -271.88769  991.2306 0.7999792
PF8-4PF14     88.485714  -543.07341  720.0448 0.9999999
PF9-4PF14   -168.014286  -799.57341  463.5448 0.9997981
Ctrl1-4PF15  266.100000  -365.45912  897.6591 0.9772709
Ctrl2-4PF15  -79.842857  -711.40198  551.7163 1.0000000
Ctrl3-4PF15  -45.571429  -677.13055  585.9877 1.0000000
Ctrl4-4PF15 -186.257143  -817.81627  445.3020 0.9993503
Ctrl5-4PF15   36.257143  -595.30198  667.8163 1.0000000
PF10-4PF15  -301.957143  -993.79550  389.8812 0.9693382
PF6-4PF15    177.357143  -454.20198  808.9163 0.9996247
PF7-4PF15    282.514286  -349.04484  914.0734 0.9624586
PF8-4PF15     11.328571  -620.23055  642.8877 1.0000000
PF9-4PF15   -245.171429  -876.73055  386.3877 0.9891118
Ctrl2-Ctrl1 -345.942857  -977.50198  285.6163 0.8408869
Ctrl3-Ctrl1 -311.671429  -943.23055  319.8877 0.9203970
Ctrl4-Ctrl1 -452.357143 -1083.91627  179.2020 0.4516451
Ctrl5-Ctrl1 -229.842857  -861.40198  401.7163 0.9941250
PF10-Ctrl1  -568.057143 -1259.89550  123.7812 0.2334219
PF6-Ctrl1    -88.742857  -720.30198  542.8163 0.9999999
PF7-Ctrl1     16.414286  -615.14484  647.9734 1.0000000
PF8-Ctrl1   -254.771429  -886.33055  376.7877 0.9845196
PF9-Ctrl1   -511.271429 -1142.83055  120.2877 0.2534495
Ctrl3-Ctrl2   34.271429  -597.28769  665.8306 1.0000000
Ctrl4-Ctrl2 -106.414286  -737.97341  525.1448 0.9999993
Ctrl5-Ctrl2  116.100000  -515.45912  747.6591 0.9999978
PF10-Ctrl2  -222.114286  -913.95264  469.7241 0.9983673
PF6-Ctrl2    257.200000  -374.35912  888.7591 0.9831446
PF7-Ctrl2    362.357143  -269.20198  993.9163 0.7914285
PF8-Ctrl2     91.171429  -540.38769  722.7306 0.9999999
PF9-Ctrl2   -165.328571  -796.88769  466.2306 0.9998326
Ctrl4-Ctrl3 -140.685714  -772.24484  490.8734 0.9999757
Ctrl5-Ctrl3   81.828571  -549.73055  713.3877 1.0000000
PF10-Ctrl3  -256.385714  -948.22407  435.4526 0.9929921
PF6-Ctrl3    222.928571  -408.63055  854.4877 0.9956581
PF7-Ctrl3    328.085714  -303.47341  959.6448 0.8864859
PF8-Ctrl3     56.900000  -574.65912  688.4591 1.0000000
PF9-Ctrl3   -199.600000  -831.15912  431.9591 0.9986191
Ctrl5-Ctrl4  222.514286  -409.04484  854.0734 0.9957382
PF10-Ctrl4  -115.700000  -807.53836  576.1384 0.9999994
PF6-Ctrl4    363.614286  -267.94484  995.1734 0.7873681
PF7-Ctrl4    468.771429  -162.78769 1100.3306 0.3907501
PF8-Ctrl4    197.585714  -433.97341  829.1448 0.9987615
PF9-Ctrl4    -58.914286  -690.47341  572.6448 1.0000000
PF10-Ctrl5  -338.214286 -1030.05264  353.6241 0.9256378
PF6-Ctrl5    141.100000  -490.45912  772.6591 0.9999749
PF7-Ctrl5    246.257143  -385.30198  877.8163 0.9886552
PF8-Ctrl5    -24.928571  -656.48769  606.6306 1.0000000
PF9-Ctrl5   -281.428571  -912.98769  350.1306 0.9636161
PF6-PF10     479.314286  -212.52407 1171.1526 0.5089848
PF7-PF10     584.471429  -107.36693 1276.3098 0.1957092
PF8-PF10     313.285714  -378.55264 1005.1241 0.9585712
PF9-PF10      56.785714  -635.05264  748.6241 1.0000000
PF7-PF6      105.157143  -526.40198  736.7163 0.9999994
PF8-PF6     -166.028571  -797.58769  465.5306 0.9998242
PF9-PF6     -422.528571 -1054.08769  209.0306 0.5683620
PF8-PF7     -271.185714  -902.74484  360.3734 0.9732704
PF9-PF7     -527.685714 -1159.24484  103.8734 0.2099093
PF9-PF8     -256.500000  -888.05912  375.0591 0.9835504

summary(res.aov)

            Df   Sum Sq Mean Sq F value Pr(>F)  
Tx          14  3431033  245074   2.138 0.0168 *
Residuals   88 10087578  114632                 
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
2 observations deleted due to missingness