From b7c0e51e3c27e473e5df01be70a6cfccb3d3ce2b Mon Sep 17 00:00:00 2001 From: dhajam <dhanaprakash.jambulingam@utu.fi> Date: Fri, 2 Jul 2021 14:52:28 +0300 Subject: [PATCH] Removed .RData and .Rhistory --- .RData | Bin 4229 -> 0 bytes .Rhistory | 201 ---------------------- rsconnect/shinyapps.io/biocpr/corplot.dcf | 4 +- 3 files changed, 2 insertions(+), 203 deletions(-) delete mode 100644 .RData delete mode 100644 .Rhistory diff --git a/.RData b/.RData deleted file mode 100644 index 929ce29797a1ac33cd52ab858bd1ae9ed17de8f0..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 4229 zcmb2|=3oE==C={mHX^V8-@g&-J;iIf^VeeCiJ_CKyId_h?uZ)hwk}iOY@MAZ7Hw6! z>xG-^q&zJzA@+rSD=z%iTk7&XM9W<%R^+eS%$rY3&b|KrtM>nof0yMqThBlL*=GLf z-#_n^)y6h0U&*@qVunfTEThR45=XRq1s}XmOLJa)aVkfWK(Al0>b|Qt_chGu@3<ks z@rg64*)7;9)8w(vqrZ1HS^qjGIFr5X_5Kwydks8)-9A2ddM=mWBdfr<KaCVl|2wp< zr}MqHbG)zbZSnKnWs9PJyjd5ub@|T+Kf_<C?au#s{<_tjfOxUjDMteMGixiR8|oIt z{{3L)UiG`9!{5r)|3FK}=NG5uE#|d)-DRpaUHwmG;@-a-+;(i-{K+@<AKT(NPhNhv ziRtRk_$>A5u-p%>m<cPTz3(04n6LTT-LgDnMW0@f7ysSMmG9=g^w_K17~So^?%HMj zjGQa4*m$@7WX<*1bx>}ryodZ|yJR1?=a>DP_q>&kW<I($=+?_1-*fv!&OP38{hQtM zz3cxiG<UXinQg6ks$DztfSv69t<q(87ta>E9hv{h&M;>w<M)Nf+9V(Al=i)qjokbp z#WASr<qE_3*KIOx{abkX#E<D~Be!2JXFnhPY=_Ivjgi(*r|F(H*rNK@^~X(K<9GIZ zBZGn^7yd1&6Wejd{!R9c8M9jYT^G(ex6bycdcW$~&G(9?nf){T^kB!D)S!-u?vMY8 zx31^QiJS3b3FnS^U;TDjrGIu~pZ4w4L-Sx|6FE-5^Urer9QpUcC^dJPPQqcy1KhLr zzn{{3xn}S4$GeyR_glVKX5$Uh-Bn+gYt?LdtH05Ab+Kz%zT>WYUb8$M{BB%3ecR~l z-49HwyX(bVSeE9WwYqMwk1NwdTjq>RneW{9S=K4<_2twp*6%vzx9iW-Mmd|$ZyH}J z&&@Jcdu=AI5!&8%Ki+Eb!*jp9OV!=ujQ-y+eOLPU4cD@_rSYG)1}{?#b60=ve*N{F z^IGd~->_5tyUp7zxZ_mqjI#fZU9WXd&-=3O`l{2h>*tBTGrY8MhJ&|{M$Gq5Tkm(o zq<txT^Wol7$!~q9^VbxV=XC#kQ)~V(=u++Mlky>QGviIK*IqOI`$%v1#-nd{Y>ZGb z&atWZIqjmU^=92;pCh*|YrU&|_xhe}KEK7;2GcwAZN%JOC7G1AtM9tDq2B#%?}Cci zO6#{9?CsoJe`cxIp5k5q+F57w?RvdT^LEHNt`n_O?7d^Zp35t|yk}Qg)#@z4Ew=kh znpUcukNI5}^4#`jJ1c+rm6_ATD*L{KOqNP{HaGVE-zRe48YN3g_joY`)wg`SvCr1x z*}LQB-7RY2_RG&o3)$tIWV!Z|>F=*wS$_@wZR&7mZ~u4orfp2khq)VeZdmwmeb(ZP zn}=sQKmL5~t_|ytExI~~%6hi?-<z(nDyFg^=@^^0<Q0>W-{&Ns7UaclzB~15<Q(7S zpZn(4R<5;)d;0CvEkm!mIOA=6;WMo@`RyiVO_BPRIqm(tL+{+(ziwIAGynJPdy#i9 zYFEYGFsYXbyLPCss5IkuO!KvueA8d}8XC@d9grWqDP_{Ow@%Y%#a?|a6Q&b2bJvb% zH@J>pJ3aMg?oGb>H;iWPT1#KQo>O^jm-~AEEg||6x8F>g)s*`-CU2FQ>*>N@vX4Xa zXOvBpI-GT<ekZs3!lSAI3GY6v$vL=qQo(oagL{6tpLWsxC7Np9d-s~zirst63U&y7 z-(XwTo*(`4h>^H(cHxHVqBVEdyjqy6*LzNso9}97u1xLvUk83_3kt7Y`Z44Bg;{>r z-v9cX#9aJu1;5vsrXX#e#?xZ&w;88<E~)6;{`H@wu?^o8%g`AaZoO+W3S+{ao?mz0 z$mUb#zkBN2V#D3O==5b6*@V8`d+NN!nx7T(eqB>(*Ep;CqUVor@Vwu$CVzrXZP=J- zAbsPevH5gPseL`w?<RJgH7hyiH}%q`u;Z3j@?u^EPhK;1X7<;rb0X&pO52z8R4=v_ zh<|Od`f2Q`um22<d1uAfX1*}8F22_Odso7y(+Yg^k}ppDlogP6M0Rd+=dx$VmAbBr z+TWb`)5`s>)ju!qNpHnp+&rTE^3bJi=DXeJoeZp&+;b}B&Z9@iA9L-!y|L^1+Nu9m zuAIH9yF07ovoV*p(B$jCQ^b4gg7zN@>}Ynj+242VZ&Fdng*>s1v(mz<gtu2dKCE?0 zHtbt<&k8lG+^Ft<-u+inWtVNO`X;P=!+5TZt)ALzt9A2tCe8WYlJ@J~7qQ*lnS5_! zC9(trH7@RSGZ#7Kchf}e*js@=miyF>B;~LM{LOyVuBfTqWt<l3w0H@h*yG1$*(p7j zmZ$&R^v1q@Wpu@_cbEFTCFU8I-Tk!fb!t?_xtPb354Ybu%5vlS8Nu%dDzC{-JLPvc zxJM^OdCmgidAFOp<x79(o(hruWp7!2IbJ2~=<_g%n0rlX5oX&Ht<Uc`BX@)&ZkBA~ zagzfojGOOSo|(VL#XJ4#t5-ihe(YbitM&NyUY<3Y+bgH8%&9*1Bk6O<*YBcFMcro~ z(s^fbX5E>vt($aY5AEEL{9(Eg_u~&|9g;%5_pF>&|9ZK%W+->u>sJN*v7GB(RfN1T zT5{`;>w=B%mS<PaK2^8c;Pr~E>zXyzOSklH{eLWZw|%>5)cOAhKHRd&Jh7u<g<q(* z@2P@)(_gv&UUOvShAAaK-rOvXx3}{wJvVhi^(&8^VHtJDSKV5D>wU&`llULE*YCbv zvq^Pz_6+{*X;rhXKe@f(^lr}CdCTVf-tf+|f8(<AJ3r^A^4{fazsq$q`LPY(-(8uV zug>Hwef?U8o%ieoXJeblvug@@w>$BLIrEuLTJ`bKjoIxbPSr)zPbp=IZIvqD+%@@b zw_5eTv;}*Q-uqCzB{Mha?eWf2reYV>7QgEEvQhq{8hd(v>&?E}$)RgAZLYrcIrJj) zP15QO+a^jLHoCa#^>wZ9agTkx>}2*DpL;EHrgp(Li`zH0EZDc~YsD(>r&|}?zLmVx zd%4<KJG;-!AyZv1vpb31E4r7Mb;bD7n#{Go`9kd-H<&(-y1H$Vbi~gc>#n%6#ea?U zy0XT%W*^_C{j-mq*}d-Fq}Q60%FKS-?1>FaV$Q!Hwe?ucX$N<Uw>M884D&KPxNwrx z)UW#`=449QJUaVX-|hWj-y<(iK71@5TQO5+*UICse_fvDy!`r^2Xk($T=cYc+thy- zw|@NAF{vp0e8=6o{?B!D^Zv$Fe0uk&QkGlMPh#_>r!Oy0Df4~5>2vzM<Er*6y(LV2 z)9vTY6F)cMjc{eQic+!L5fz*3H@23w7{@8-Cf0x5T3MLB{&A1;Ydr_|)4k8GuJpGQ z-L9N5;qis^#8}1Iyv)(wV!MxpZ;|=&de4rk=mS@l3hulpE}O0@Be_S(!20E)Z%;Rc zCLVA<&MEa<&h*otL)+ILUwuA4kn6F{jcMPF*e&Ly&WL4N{%*g0X_do-^Ox4APMr2K zx#+uWY*_+(`rBE-tL>vKUl_N|%KrD&=KGGL_dcv>juvk_xA#co|7BYXZ^k4ZI=Zak zHTTSS@2>=2o&9}!RK(sD+BVBhR@*iD8h7W*9Gq3P=v&*)&c}Byik}g-x&O{);>qft zQ%{y(_Vu!S^3hAc<k!h7#c#|FU#R`RqWm_C-RKp+SdY*T?zv09<{kL<r|-h{fCKN- ztaZ(#>z1yaSO0VAP0iJ;k>83xonkgRl{2y0<InR6{&&pzr2X?Y-?uHe_Snf|2g?Ij zMkWE}4BtnRm$ol^s3N9p(cs*1qm}!sVdxyi7VZRv%6STvn;i{1oNU(gAD{8|?6czE z9M@z74ybOJ5))FW-gY`J_P%GR{b`2@?aCTk{UlVFYChTp`8u5FYe|rC`EB9j;qryi z%bw?f#S!M%#|0t^l^j|L=MUak;E;FBeBSgG^7$Pstg0G^m<@ZH7d&7{k;w69P(GuO z_VgdOv$CQggLAi|{Ue1&-}O`PPup+%cUzy-22%l--+mcdS(_4WZ_@3UF8AoAoPyKL zvuVQd^M6m9$>rTVO+em@d4`V6)Ix?i>QmOQtoeJ;PF3R*dyJX{d!og)?Ta#=+~4~y zT`jid!$C&(h>1al{QuwO_s2;7&6dCW{foP-OCXEvi^)w2OBvax9I#-m_;)s0R4~y} z@R@zVxdX8ZZUG)T7yd4b6My(|iN=ZRtw(m<Uv!{i(%g6aDyx_!W~;LVG+dXScmG;D zPr<v}Gv#jCTiZx9B+6_3pHj8<mcJCwhXePns01?XTdpkm%ihnQp?ea8#7y6;BibF0 zb_gg4drkHBn4+N3cT!R!BbBqOQf1M(;<`DnrS|T8$97PG{Q>9ywG2G(o>np@9a0aO z=-T$5-#B(A_r&!)kFK7Y#N*lIpt2;xO5AP76>F|zliVv<`j!}l9<qs>;=wo7h`((` zuYro9`6@vcHQ_?R8B9Ix2V4x564;;0Oym&kW|*>zLoQIaMS)dwZu^mdtDWskMyFgu z<+>6i_znbK3De}7-1L)yZ$n`NcW~M+i`|ope#CI<C@;PAQ^75cznlNqgN{2%YVt}> z?W?BO9BJq9kYMvP<=NMypekO!>Bq;^BnOs{e*y)bc$|E!BcS%+phC~0WQGVW_DO=A z9fm?)X(|oJPUKrm@(_^=eDQQ?)Y9pyOe!Lt58PV#Ja;Ls@Zg#p8m&3$m3&iN%D<hA z0y6OpCH}4o6Ap0XIeH0lXle@NIWlTAES<vN_0}`A!Kvoxvx6cU_c$Ci9oAl}e%WI0 zvSYH}Y0D+7%+hks9GopnWP2=?I(B)cF6{7fQq*huD=Jc-tno_j&gqWUA50TY#Vivz zu6jx0l55ki!v2u9BO#S9?$?GY^mr5)&JW=d)L`a1J7b>*6PL$+vBVCEwkHb(RNFLK zbtE1%83a0<bX}wyEdFh=oUcrT&TC%1AX6UKCL76qrUq4}j@1))A9>~LU?=3Q=)c6A z>*!BG)(M~7SUwpVNKKur#Ik6Wcq~h&Lzbu3v5o+BPZy>x!yc9Y>pwSp<rliGG&=C1 z@RLy23F!$A20Q`Byce;=XtD%52%GQ=x;rs>g-l^^V<?KfdAwPNg-2-@YlwvQl1-ah zoMvk}GVWZ=e0-MO9uB>}(@Tyl4Lo^wyS87W*aC%RJN#O-MRmPGMAJN$Xn3ja(~o9( z<kZst(^vWJmsDkrm$USvyPQL0w0}lTd=%)Q^w2qE!^%ZAg8!qRsu_NN`b8``ebK4l zjV|AxdY-5{^x^4=)tb#3x;61$CK|8iHlCOhqL{(5Tqe-%pv9?O@qhO`-&GwPl+e%= zDk>{btRvDnne)lYbzMRnx=w;ES?e_1Vph+P$k6;)_u1yD<>I!a9aH!f8(0?k9jVFh z`fnj%Y`AD^;4=PW`}*T2SWIG>(a5Q|u_xq5Z^5_M?s}8vzf&z#)Cdyj@CcM!5s?*Q zu%}$C>DT0tJBdbG4jdk$>D+33g-=y|c-wy%DV-L%aG-kY>5bEqT<!$yZPPodoa-?^ zsba?;bw?f-k<6_75A1>%!`&|AoQqK}s@737?&^|o(`gC*I$h4aXVMbogK_gjqFE+S zKh^PiE!z_J!mhgwddw~#4m3`EvFM8a^7)f*pFjEb`4cy*FU3W#FMla6`fa)M@0>ez zetGul+y8%h@@;$leUpx5`f@-1Z~yjR+qO>R^WR4?2Vd1K?(zD6?f3iUWBbnwF#jsq sUuLu5u9n%{I^IMF&rqG1dhgZ$1pm!%Esj?aDF3p5Gw;^!)k+Ku0J(ZUP5=M^ diff --git a/.Rhistory b/.Rhistory deleted file mode 100644 index 2aed2d4..0000000 --- a/.Rhistory +++ /dev/null @@ -1,201 +0,0 @@ -shiny::runApp('corplot') -shiny::runApp('corplot') -c -tumor_expression_plot_Christoffer <- read.delim("~/tumor_expression_plot_Christoffer.txt", row.names=1) -View(tumor_expression_plot_Christoffer) -cormat<-signif(cor(tumor_expression_plot_Christoffer),2) -cormat -View(cormat) -col<- colorRampPalette(c("blue", "white", "red"))(20) -heatmap(cormat, col=col, symm=TRUE) -cormat<-signif(cor(tumor_expression_plot_Christoffer),1) -View(cormat) -cormat<-signif(cor(1,tumor_expression_plot_Christoffer)) -cormat<-signif(1,cor(tumor_expression_plot_Christoffer)) -View(cormat) -cormat<-signif(cor(tumor_expression_plot_Christoffer)) -View(cormat) -dist(tumor_expression_plot_Christoffer) -cor(tumor_expression_plot_Christoffer) -cor(tumor_expression_plot_Christoffer,2) -cor(tumor_expression_plot_Christoffer),2 -cor(tumor_expression_plot_Christoffer) -runApp('corplot') -runApp('Downloads/shinyCorrplot-gh-pages') -shiny::runApp('corplot') -runApp('corplot') -runApp('corplot') -runApp('corplot') -runApp('corplot') -runApp('corplot') -runApp('corplot') -runApp('corplot') -shiny::runApp('corplot') -shiny::runApp('corplot') -shiny::runApp('corplot') -runApp('corplot') -shiny::runApp('corplot') -install.packages("h5") -shiny::runApp('corplot') -shiny::runApp('publication/corplot') -?cormat -?cormap2 -shiny::runApp('publication/corplot') -shiny::runApp('publication/corplot') -?cormap2 -runApp('publication/corplot') -library(coreheat) -?cormap2 -shiny::runApp('publication/corplot') -runApp('publication/corplot') -?citation -citation(package = "ggcorrplot") -library(ggcorrplot) -install.packages("ggcorrplot") -library(ggcorrplot) -citation(package = "ggcorrplot") -install.packages("graphics") -install.packages("graphics") -install.packages("graphics") -install.packages("graphics") -install.packages("graphics") -library(graphics) -??graphics -?graphics -install.packages("dataSet") -install.packages("grDevices") -install.packages("grDevices") -install.packages("grDevices") -library(grDevices) -?grDevices -library(grid) -?grid -install.packages("dataset") -install.packages("altset") -q -quit -exit -citation() -citation(package = "ggally") -install.packages("ggally") -install.packages("GGally") -library(GGally) -citation(package = "GGally") -citation(package = "corrplot") -citation(package = "GGally") -citation() -citation(package = "ggcorrplot") -citation(package = "shiny") -library("coreheat") -?cormap2 -shiny::runApp('publication/corplot') -library(corrplot) -library(coreheat) -?coreheat -library(coreheat) -?coreheat -library(heatmapGen2) -?heatmapGen2 -.libPaths() -.libPaths() -myLibraryLocation <- .libPaths()[1] -cranPackages <- c("shinyBS", "shinythemes", "knitr", "rmarkdown", "shinyjs", "plyr", "RColorBrewer", "R.utils", "gdata", "data.table", "foreach", "ggplot2", "scales", "curl", "openssl", "httr", "Rcurl", "XML", "WGCNA") -sapply(cranPackages, install.packages, lib = myLibraryLocation) -bioConPackages <- c("AnnotationDbi", "biomaRt", "org.Hs.eg.db", "org.Mm.eg.db", "Heatplus", "genefilter", "impute", "preprocessCore", "Go.db") -if (!requireNamespace("BiocManager", quietly = TRUE)) -install.packages("BiocManager") -BiocManager::install(bioConPackages) -install.packages("/home/dhajam/publication/corplot/packages/coreheat_0.1.0_R_x86_64-pc-linux-gnu.tar.gz", repos = NULL, type="source") -library(coreheat) -install.packages('rsconnect') -rsconnect::setAccountInfo(name='biocpr', -token='D7412524543BF89B036143D3FB9F8A57', -secret='<SECRET>') -rsconnect::setAccountInfo(name='biocpr', -token='D7412524543BF89B036143D3FB9F8A57', -secret='SHRyvzmyM0DRFzfxbuChXTZq7uxP7qcGdO3kw+XX') -rsconnect::setAccountInfo(name='biocpr', -token='D7412524543BF89B036143D3FB9F8A57', -secret='SHRyvzmyM0DRFzfxbuChXTZq7uxP7qcGdO3kw+XX') -lucid$currentUser() -library(rsconnect) -rsconnect::setAccountInfo(name='biocpr', -token='D7412524543BF89B036143D3FB9F8A57', -secret='SHRyvzmyM0DRFzfxbuChXTZq7uxP7qcGdO3kw+XX') -rsconnect::setAccountInfo(name='biocpr', -token='D7412524543BF89B036143D3FB9F8A57', -secret='SHRyvzmyM0DRFzfxbuChXTZq7uxP7qcGdO3kw+XX') -shiny::runApp('publication/corplot') -runApp('publication/corplot') -runApp('publication/corplot') -runApp('/home/dhajam/publication/corplot') -library(rsconnect) -rsconnect::deployApp('/home/dhajam/publication/corplot') -shiny::runApp('publication/corplot') -shiny::runApp('publication/corplot') -rsconnect::deployApp('/home/dhajam/publication/corplot') -runApp('publication/corplot') -runApp('publication/corplot') -shiny::runApp() -runApp() -rsconnect::deployApp('/home/dhajam/publication/corplot') -rsconnect::deployApp('/home/dhajam/publication/corplot') -allPackages <- installed.packages() -allPackages <- allPackages[ is.na(allPackages[,4]), 1] -sapply(allPackages, remove.packages) -shiny::runApp() -runApp() -rsconnect::deployApp('/home/dhajam/publication/corplot') -install.packages("rsconnect") -install.packages("rsconnect") -rsconnect::deployApp('/home/dhajam/publication/corplot') -rsconnect::deployApp('/home/dhajam/publication/corplot') -rsconnect::deployApp('/home/dhajam/publication/corplot') -rsconnect::appDependencies('/home/dhajam/publication/corplot') -if (!requireNamespace("BiocManager", quietly = TRUE)) -install.packages("BiocManager") -installed.packages() -devtools::install_github("cancer-genetics-utu/readR") -install -install.packages("devtools") -devtools::install_github("cancer-genetics-utu/readR") -rsconnect::deployApp('/home/dhajam/publication/corplot') -devtools::install_github("cancer-genetics-utu/medseqr") -devtools::install_github("cancer-genetics-utu/coreheat") -devtools::install_github("cancer-genetics-utu/genRal") -devtools::install_github("cancer-genetics-utu/heatmapGen") -devtools::install_github("cancer-genetics-utu/heatmapGen2") -devtools::install_github("cancer-genetics-utu/PAMhm") -cran_packages <- c("R.methodsS3", "R.oo", "R.utils", "RColorBrewer", "RCurl", "XML", "clipr", "cluster", "curl", "data.table","devtools", "digest", "foreach", "gdata", "ggplot2", "httr", "knitr", "openssl", "plyr", "rmarkdown", "scales", "shiny", "shinyBS", "shinyjs", "shinythemes", "WGCNA") -bio_packages <- c("AnnotationDbi", "Biobase", "BiocGenerics", "GO.db", "Heatplus", "IRanges", "S4Vectors", "biomaRt", "genefilter", "impute", "latticeExtra", "org.Hs.eg.db", "org.Mm.eg.db", "preprocessCore") -sapply(cran_packages, install.packages) -if (!requireNamespace("BiocManager", quietly = TRUE)) -install.packages("BiocManager") -BiocManager::install(bio_packages) -install.packages("impute") -BiocManager::install("impute") -install.packages("WGCNA") -rsconnect::deployApp('/home/dhajam/publication/corplot') -devtools::install_github("cancer-genetics-utu/readR") -devtools::install_github("cancer-genetics-utu/medseqr") -devtools::install_github("cancer-genetics-utu/coreheat") -devtools::install_github("cancer-genetics-utu/genRal") -devtools::install_github("cancer-genetics-utu/heatmapGen") -devtools::install_github("cancer-genetics-utu/heatmapGen2") -devtools::install_github("cancer-genetics-utu/PAMhm") -devtools::install_github("cancer-genetics-utu/medseqr") -rsconnect::deployApp('/home/dhajam/publication/corplot') -BiocManager::install("Heatplus") -rsconnect::deployApp('/home/dhajam/publication/corplot') -options(repos = BiocManager::repositories()) -getOption("repos") -rsconnect::deployApp('/home/dhajam/publication/corplot') -options(repos="https://CRAN.R-project.org") -getOption("repos") -options(repos = BiocManager::repositories()) -getOption("repos") -rsconnect::deployApp('/home/dhajam/publication/corplot') -options(repos = "https://CRAN.R-project.org") -getOption("repos") -options(repos = BiocManager::repositories()) -rsconnect::deployApp('/home/dhajam/publication/corplot') diff --git a/rsconnect/shinyapps.io/biocpr/corplot.dcf b/rsconnect/shinyapps.io/biocpr/corplot.dcf index 9665cde..1497ee8 100644 --- a/rsconnect/shinyapps.io/biocpr/corplot.dcf +++ b/rsconnect/shinyapps.io/biocpr/corplot.dcf @@ -5,6 +5,6 @@ account: biocpr server: shinyapps.io hostUrl: https://api.shinyapps.io/v1 appId: 2285412 -bundleId: 3220865 +bundleId: 4780472 url: https://biocpr.shinyapps.io/corplot/ -when: 1591145681.80498 +when: 1625226629.75996 -- GitLab