## Warning: package 'agricolae' was built under R version 3.4.2
## Warning: package 'DescTools' was built under R version 3.4.2
## Warning: package 'tidyverse' was built under R version 3.4.2
## Loading tidyverse: tibble
## Loading tidyverse: tidyr
## Loading tidyverse: readr
## Loading tidyverse: purrr
## Loading tidyverse: dplyr
## Warning: package 'tidyr' was built under R version 3.4.2
## Warning: package 'readr' was built under R version 3.4.2
## Warning: package 'purrr' was built under R version 3.4.2
## Conflicts with tidy packages ----------------------------------------------
## filter(): dplyr, stats
## lag(): dplyr, stats
## Warning: package 'plotly' was built under R version 3.4.2
##
## Attaching package: 'plotly'
## The following object is masked from 'package:ggplot2':
##
## last_plot
## The following object is masked from 'package:stats':
##
## filter
## The following object is masked from 'package:graphics':
##
## layout
## Warning: package 'highcharter' was built under R version 3.4.2
## Highcharts (www.highcharts.com) is a Highsoft software product which is
## not free for commercial and Governmental use
## Df Sum Sq Mean Sq F value Pr(>F)
## lipid 12 116780 9732 149.3 <2e-16 ***
## Residuals 26 1695 65
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Study: fit ~ "lipid"
##
## Duncan's new multiple range test
## for calcein_release
##
## Mean Square Error: 65.17978
##
## lipid, means
##
## calcein_release std r Min Max
## 5_cholesten_3_on 94.69041 4.455524 3 89.94321 98.78150
## 7_dehydrocholesterol 82.14833 6.479364 3 75.34990 88.25275
## B_sitosterol 66.08373 6.209162 3 58.94449 70.22534
## CPE_Chol_POPC_1_49_5_49_5 82.92644 9.961909 3 74.19453 93.77737
## CPE_Chol_POPC_20_40_40 272.09874 18.830082 3 251.55985 288.54779
## CPE_Chol_POPC_40_30_30 89.68280 6.850187 3 82.52746 96.18038
## ergoterol 90.38609 2.589645 3 88.52638 93.34384
## lanosterol 86.71337 5.292523 3 81.50305 92.08443
## POPC 80.73930 10.164328 3 74.14613 92.44488
## POPC_Chol 69.87591 5.771182 3 64.56301 76.01609
## POPC_SM 31.17688 1.145309 3 30.15805 32.41652
## SM_Chol 111.77590 6.591109 3 107.18341 119.32804
## stigmasterol 61.44981 5.488280 3 55.17995 65.38337
##
## Alpha: 0.05 ; DF Error: 26
##
## Critical Range
## 2 3 4 5 6 7 8 9
## 13.54985 14.23459 14.67588 14.98887 15.22355 15.40598 15.55137 15.66933
## 10 11 12 13
## 15.76630 15.84677 15.91401 15.97044
##
## Means with the same letter are not significantly different.
##
## calcein_release groups
## CPE_Chol_POPC_20_40_40 272.09874 a
## SM_Chol 111.77590 b
## 5_cholesten_3_on 94.69041 c
## ergoterol 90.38609 c
## CPE_Chol_POPC_40_30_30 89.68280 c
## lanosterol 86.71337 c
## CPE_Chol_POPC_1_49_5_49_5 82.92644 cd
## 7_dehydrocholesterol 82.14833 cd
## POPC 80.73930 cde
## POPC_Chol 69.87591 def
## B_sitosterol 66.08373 ef
## stigmasterol 61.44981 f
## POPC_SM 31.17688 g
##
## Posthoc multiple comparisons of means : Newman-Keuls
## 95% family-wise confidence level
## factor levels have been ordered
##
## $lipid
## diff lwr.ci
## stigmasterol-POPC_SM 30.2729337 16.7230833
## B_sitosterol-POPC_SM 34.9068500 18.5266713
## POPC_Chol-POPC_SM 38.6990253 20.6153271
## POPC-POPC_SM 49.5624188 30.2583544
## 7_dehydrocholesterol-POPC_SM 50.9714518 30.7181278
## CPE_Chol_POPC_1_49_5_49_5-POPC_SM 51.7495607 30.7207674
## lanosterol-POPC_SM 55.5364908 33.8531095
## CPE_Chol_POPC_40_30_30-POPC_SM 58.5059218 36.2568453
## ergoterol-POPC_SM 59.2092118 36.4625169
## 5_cholesten_3_on-POPC_SM 63.5135311 40.3229933
## SM_Chol-POPC_SM 80.5990163 57.0081658
## CPE_Chol_POPC_20_40_40-POPC_SM 240.9218601 216.9666386
## B_sitosterol-stigmasterol 4.6339163 -8.9159342
## POPC_Chol-stigmasterol 8.4260915 -7.9540872
## POPC-stigmasterol 19.2894851 1.2057870
## 7_dehydrocholesterol-stigmasterol 20.6985180 1.3944536
## CPE_Chol_POPC_1_49_5_49_5-stigmasterol 21.4766270 1.2233030
## lanosterol-stigmasterol 25.2635571 4.2347637
## CPE_Chol_POPC_40_30_30-stigmasterol 28.2329880 6.5496068
## ergoterol-stigmasterol 28.9362781 6.6872016
## 5_cholesten_3_on-stigmasterol 33.2405974 10.4939024
## SM_Chol-stigmasterol 50.3260826 27.1355448
## CPE_Chol_POPC_20_40_40-stigmasterol 210.6489263 187.0580758
## POPC_Chol-B_sitosterol 3.7921752 -9.7576752
## POPC-B_sitosterol 14.6555688 -1.7246099
## 7_dehydrocholesterol-B_sitosterol 16.0646017 -2.0190964
## CPE_Chol_POPC_1_49_5_49_5-B_sitosterol 16.8427107 -2.4613538
## lanosterol-B_sitosterol 20.6296408 0.3763167
## CPE_Chol_POPC_40_30_30-B_sitosterol 23.5990717 2.5702784
## ergoterol-B_sitosterol 24.3023618 2.6189805
## 5_cholesten_3_on-B_sitosterol 28.6066811 6.3576046
## SM_Chol-B_sitosterol 45.6921663 22.9454714
## CPE_Chol_POPC_20_40_40-B_sitosterol 206.0150100 182.8244722
## POPC-POPC_Chol 10.8633936 -2.6864569
## 7_dehydrocholesterol-POPC_Chol 12.2724265 -4.1077522
## CPE_Chol_POPC_1_49_5_49_5-POPC_Chol 13.0505354 -5.0331627
## lanosterol-POPC_Chol 16.8374655 -2.4665989
## CPE_Chol_POPC_40_30_30-POPC_Chol 19.8068965 -0.4464275
## ergoterol-POPC_Chol 20.5101865 -0.5186068
## 5_cholesten_3_on-POPC_Chol 24.8145058 3.1311246
## SM_Chol-POPC_Chol 41.8999910 19.6509145
## CPE_Chol_POPC_20_40_40-POPC_Chol 202.2228348 179.4761399
## 7_dehydrocholesterol-POPC 1.4090329 -12.1408175
## CPE_Chol_POPC_1_49_5_49_5-POPC 2.1871419 -14.1930369
## lanosterol-POPC 5.9740719 -12.1096262
## CPE_Chol_POPC_40_30_30-POPC 8.9435029 -10.3605615
## ergoterol-POPC 9.6467930 -10.6065310
## 5_cholesten_3_on-POPC 13.9511123 -7.0776811
## SM_Chol-POPC 31.0365975 9.3532162
## CPE_Chol_POPC_20_40_40-POPC 191.3594412 169.1103647
## CPE_Chol_POPC_1_49_5_49_5-7_dehydrocholesterol 0.7781089 -12.7717415
## lanosterol-7_dehydrocholesterol 4.5650390 -11.8151397
## CPE_Chol_POPC_40_30_30-7_dehydrocholesterol 7.5344700 -10.5492281
## ergoterol-7_dehydrocholesterol 8.2377600 -11.0663044
## 5_cholesten_3_on-7_dehydrocholesterol 12.5420793 -7.7112447
## SM_Chol-7_dehydrocholesterol 29.6275645 8.5987712
## CPE_Chol_POPC_20_40_40-7_dehydrocholesterol 189.9504083 168.2670270
## lanosterol-CPE_Chol_POPC_1_49_5_49_5 3.7869301 -9.7629204
## CPE_Chol_POPC_40_30_30-CPE_Chol_POPC_1_49_5_49_5 6.7563611 -9.6238177
## ergoterol-CPE_Chol_POPC_1_49_5_49_5 7.4596511 -10.6240470
## 5_cholesten_3_on-CPE_Chol_POPC_1_49_5_49_5 11.7639704 -7.5400940
## SM_Chol-CPE_Chol_POPC_1_49_5_49_5 28.8494556 8.5961316
## CPE_Chol_POPC_20_40_40-CPE_Chol_POPC_1_49_5_49_5 189.1722994 168.1435060
## CPE_Chol_POPC_40_30_30-lanosterol 2.9694310 -10.5804195
## ergoterol-lanosterol 3.6727210 -12.7074577
## 5_cholesten_3_on-lanosterol 7.9770403 -10.1066578
## SM_Chol-lanosterol 25.0625255 5.7584611
## CPE_Chol_POPC_20_40_40-lanosterol 185.3853693 165.1320453
## ergoterol-CPE_Chol_POPC_40_30_30 0.7032901 -12.8465604
## 5_cholesten_3_on-CPE_Chol_POPC_40_30_30 5.0076093 -11.3725694
## SM_Chol-CPE_Chol_POPC_40_30_30 22.0930945 4.0093964
## CPE_Chol_POPC_20_40_40-CPE_Chol_POPC_40_30_30 182.4159383 163.1118739
## 5_cholesten_3_on-ergoterol 4.3043193 -9.2455312
## SM_Chol-ergoterol 21.3898045 5.0096257
## CPE_Chol_POPC_20_40_40-ergoterol 181.7126482 163.6289501
## SM_Chol-5_cholesten_3_on 17.0854852 3.5356347
## CPE_Chol_POPC_20_40_40-5_cholesten_3_on 177.4083290 161.0281502
## CPE_Chol_POPC_20_40_40-SM_Chol 160.3228438 146.7729933
## upr.ci pval
## stigmasterol-POPC_SM 43.82278 9.9e-05 ***
## B_sitosterol-POPC_SM 51.28703 4.5e-05 ***
## POPC_Chol-POPC_SM 56.78272 2.0e-05 ***
## POPC-POPC_SM 68.86648 5.3e-07 ***
## 7_dehydrocholesterol-POPC_SM 71.22478 4.7e-07 ***
## CPE_Chol_POPC_1_49_5_49_5-POPC_SM 72.77835 4.9e-07 ***
## lanosterol-POPC_SM 77.21987 1.7e-07 ***
## CPE_Chol_POPC_40_30_30-POPC_SM 80.75500 7.9e-08 ***
## ergoterol-POPC_SM 81.95591 7.7e-08 ***
## 5_cholesten_3_on-POPC_SM 86.70407 2.3e-08 ***
## SM_Chol-POPC_SM 104.18987 1.7e-10 ***
## CPE_Chol_POPC_20_40_40-POPC_SM 264.87708 3.0e-14 ***
## B_sitosterol-stigmasterol 18.18377 0.4883
## POPC_Chol-stigmasterol 24.80627 0.4197
## POPC-stigmasterol 37.37318 0.0334 *
## 7_dehydrocholesterol-stigmasterol 40.00258 0.0312 *
## CPE_Chol_POPC_1_49_5_49_5-stigmasterol 41.72995 0.0330 *
## lanosterol-stigmasterol 46.29235 0.0112 *
## CPE_Chol_POPC_40_30_30-stigmasterol 49.91637 0.0047 **
## ergoterol-stigmasterol 51.18535 0.0045 **
## 5_cholesten_3_on-stigmasterol 55.98729 0.0011 **
## SM_Chol-stigmasterol 73.51662 2.0e-06 ***
## CPE_Chol_POPC_20_40_40-stigmasterol 234.23978 3.0e-14 ***
## POPC_Chol-B_sitosterol 17.34203 0.5700
## POPC-B_sitosterol 31.03575 0.0859 .
## 7_dehydrocholesterol-B_sitosterol 34.14830 0.0948 .
## CPE_Chol_POPC_1_49_5_49_5-B_sitosterol 36.14678 0.1091
## lanosterol-B_sitosterol 40.88296 0.0441 *
## CPE_Chol_POPC_40_30_30-B_sitosterol 44.62787 0.0205 *
## ergoterol-B_sitosterol 45.98574 0.0202 *
## 5_cholesten_3_on-B_sitosterol 50.85576 0.0051 **
## SM_Chol-B_sitosterol 68.43886 9.1e-06 ***
## CPE_Chol_POPC_20_40_40-B_sitosterol 229.20555 3.0e-14 ***
## POPC-POPC_Chol 24.41324 0.1114
## 7_dehydrocholesterol-POPC_Chol 28.65261 0.1700
## CPE_Chol_POPC_1_49_5_49_5-POPC_Chol 31.13423 0.2213
## lanosterol-POPC_Chol 36.14153 0.1092
## CPE_Chol_POPC_40_30_30-POPC_Chol 40.06022 0.0580 .
## ergoterol-POPC_Chol 41.53898 0.0594 .
## 5_cholesten_3_on-POPC_Chol 46.49789 0.0168 *
## SM_Chol-POPC_Chol 64.14907 3.1e-05 ***
## CPE_Chol_POPC_20_40_40-POPC_Chol 224.96953 3.0e-14 ***
## 7_dehydrocholesterol-POPC 14.95888 0.8324
## CPE_Chol_POPC_1_49_5_49_5-POPC 18.56732 0.9413
## lanosterol-POPC 24.05777 0.8016
## CPE_Chol_POPC_40_30_30-POPC 28.24757 0.6595
## ergoterol-POPC 29.90012 0.6893
## 5_cholesten_3_on-POPC 34.97991 0.3729
## SM_Chol-POPC 52.71998 0.0016 **
## CPE_Chol_POPC_20_40_40-POPC 213.60852 3.0e-14 ***
## CPE_Chol_POPC_1_49_5_49_5-7_dehydrocholesterol 14.32796 0.9069
## lanosterol-7_dehydrocholesterol 20.94522 0.7699
## CPE_Chol_POPC_40_30_30-7_dehydrocholesterol 25.61817 0.6669
## ergoterol-7_dehydrocholesterol 27.54182 0.7230
## 5_cholesten_3_on-7_dehydrocholesterol 32.79540 0.4229
## SM_Chol-7_dehydrocholesterol 50.65636 0.0022 **
## CPE_Chol_POPC_20_40_40-7_dehydrocholesterol 211.63379 3.0e-14 ***
## lanosterol-CPE_Chol_POPC_1_49_5_49_5 17.33678 0.5706
## CPE_Chol_POPC_40_30_30-CPE_Chol_POPC_1_49_5_49_5 23.13654 0.5681
## ergoterol-CPE_Chol_POPC_1_49_5_49_5 25.54335 0.6738
## 5_cholesten_3_on-CPE_Chol_POPC_1_49_5_49_5 31.06803 0.4034
## SM_Chol-CPE_Chol_POPC_1_49_5_49_5 49.10278 0.0022 **
## CPE_Chol_POPC_20_40_40-CPE_Chol_POPC_1_49_5_49_5 210.20109 3.0e-14 ***
## CPE_Chol_POPC_40_30_30-lanosterol 16.51928 0.6561
## ergoterol-lanosterol 20.05290 0.8437
## 5_cholesten_3_on-lanosterol 26.06074 0.6261
## SM_Chol-lanosterol 44.36659 0.0064 **
## CPE_Chol_POPC_20_40_40-lanosterol 205.63869 3.0e-14 ***
## ergoterol-CPE_Chol_POPC_40_30_30 14.25314 0.9159
## 5_cholesten_3_on-CPE_Chol_POPC_40_30_30 21.38779 0.7306
## SM_Chol-CPE_Chol_POPC_40_30_30 40.17679 0.0124 *
## CPE_Chol_POPC_20_40_40-CPE_Chol_POPC_40_30_30 201.72000 3.0e-14 ***
## 5_cholesten_3_on-ergoterol 17.85417 0.5195
## SM_Chol-ergoterol 37.76998 0.0087 **
## CPE_Chol_POPC_20_40_40-ergoterol 199.79635 3.0e-14 ***
## SM_Chol-5_cholesten_3_on 30.63534 0.0155 *
## CPE_Chol_POPC_20_40_40-5_cholesten_3_on 193.78851 3.0e-14 ***
## CPE_Chol_POPC_20_40_40-SM_Chol 173.87269 3.0e-14 ***
##
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## Df Sum Sq Mean Sq F value Pr(>F)
## lipid 3 3643 1214.4 80.64 2.55e-06 ***
## Residuals 8 120 15.1
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Study: fit ~ "lipid"
##
## Duncan's new multiple range test
## for calcein_release
##
## Mean Square Error: 15.05977
##
## lipid, means
##
## calcein_release std r Min Max
## POPC 91.96440 3.143118 3 88.46586 94.54993
## POPC_Chol 104.44602 4.712804 3 99.73570 109.16130
## POPC_SM 56.92111 4.247431 3 53.51105 61.67889
## SM_Chol 84.98570 3.179418 3 81.93785 88.28210
##
## Alpha: 0.05 ; DF Error: 8
##
## Critical Range
## 2 3 4
## 7.306740 7.614313 7.786229
##
## Means with the same letter are not significantly different.
##
## calcein_release groups
## POPC_Chol 104.44602 a
## POPC 91.96440 b
## SM_Chol 84.98570 b
## POPC_SM 56.92111 c
##
## Posthoc multiple comparisons of means : Newman-Keuls
## 95% family-wise confidence level
## factor levels have been ordered
##
## $lipid
## diff lwr.ci upr.ci pval
## SM_Chol-POPC_SM 28.064593 20.7578532 35.37133 2.1e-05 ***
## POPC-POPC_SM 35.043298 25.9892811 44.09732 1.0e-05 ***
## POPC_Chol-POPC_SM 47.524911 37.3780289 57.67179 1.9e-06 ***
## POPC-SM_Chol 6.978706 -0.3280339 14.28545 0.05877 .
## POPC_Chol-SM_Chol 19.460318 10.4063010 28.51434 0.00071 ***
## POPC_Chol-POPC 12.481613 5.1748731 19.78835 0.00430 **
##
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
klc<-ggplot(mcrA11, aes(x=V3, y=calcein_release, fill=as.factor(V3)))+
geom_bar(stat = 'identity')+
scale_fill_hue(c=40, h =c(0,360), direction = 1, l= 80, h.start = 0, ('lipids'), labels=c(mcrA11$lipid))+
theme_classic()+
scale_y_continuous(name="% of calcein release")+
theme(axis.text.x = element_text( angle = 60, hjust = 1), legend.position = 'none',axis.title.x=element_blank() )+
expand_limits( y = c(0,300))+
scale_x_continuous(labels = c(as.character(mcrA11$lipid)), breaks=c(mcrA11$V3) )+
geom_errorbar(aes(x=V3, ymin=calcein_release-V4 ,ymax=calcein_release+V4), width=0.5, linetype = 1, alpha= 0.5)+
annotate('text', x=c(mcrA11$V3), y=c(mcrA11$calcein_release)+30, label= c('a','b','c','c','c','c','cd','cd','cde','def','ef','f','g'), alpha=0.5)
klc
ggplot(mcrA11, aes( x=V3, y=calcein_release, fill=as.factor(lipid)))+
geom_bar(stat = 'identity')
ggplotly(
layout =c(
autosize=F,
width=10,
height=500,
margin=go.Margin(
l=50,
r=50,
b=200,
t=8,
pad=1)),
klc
)
## We recommend that you use the dev version of ggplot2 with `ggplotly()`
## Install it with: `devtools::install_github('hadley/ggplot2')`
