From b9ff5710333dc0e5d388c7f3472f700adbce7eaf Mon Sep 17 00:00:00 2001 From: Xiao Chen Date: Tue, 19 May 2020 09:29:26 -0700 Subject: [PATCH] Added an example output for visualization tool --- README.md | 2 +- charts/data/smn_HG03458.pdf | Bin 0 -> 10343 bytes 2 files changed, 1 insertion(+), 1 deletion(-) create mode 100644 charts/data/smn_HG03458.pdf diff --git a/README.md b/README.md index b968fa1..a5dc3e2 100755 --- a/README.md +++ b/README.md @@ -56,5 +56,5 @@ A visualization tool for the SMNCopyNumberCaller result takes the .json file pro smn_charts.py -s SMN_JSON_FILE \ -o OUTPUT_DIRECTORY ``` -A .pdf file is produced for each sample in OUTPUT_DIRECTORY, containing four plots. The first two plots show where the raw depth values (vertical lines) stand against the population samples for the total SMN CN and the full length SMN CN. The third plot shows the raw CN values for SMN1 and SMN2 at 8 sites that we use to determine the consensus. #13 is the splice variant site. The last plot shows the raw read counts for SMN1 and SMN2 on the right y axis and the left y axis is a rough calculation of CN: #reads divided by the median haploid depth. +A .pdf file is produced for each sample in OUTPUT_DIRECTORY, containing four plots. The first two plots show where the raw depth values (vertical lines) stand against the population samples for the total SMN CN and the full length SMN CN. The third plot shows the raw CN values for SMN1 and SMN2 at 8 sites that we use to determine the consensus. #13 is the splice variant site. The last plot shows the raw read counts for SMN1 and SMN2 on the right y axis and the left y axis is a rough calculation of CN: #reads divided by the median haploid depth. An example can be found [here](https://github.com/Illumina/SMNCopyNumberCaller/blob/master/charts/data/smn_HG03458.pdf). diff --git a/charts/data/smn_HG03458.pdf b/charts/data/smn_HG03458.pdf new file mode 100644 index 0000000000000000000000000000000000000000..283a65f8a7fb7f4ab612b8a1eddd4417d27c9a80 GIT binary patch literal 10343 zcma)iS=*{WlIH#S6`!aqA}XjLps0WwE{KQ04flV+^mgewF|C|N5W*=V#+*>Fcwwou7%H_%Hk8dq26xkC(dN z*iSw`_s=I|>h-_;TCP;8&>My^fvxG{k~lP{qq~f(Z75q>L>TX zpVn=&csKss3B#YM*NZGVAjaL%bI`J`z`w;{saAQ$K^v@zfxEA zKlupjza3uR`u~!J-;b85m-|e6`>Qm`Z+?s3e?#Km{3+NUJ4$c=V1xVz8^iDCp1ywIBWx#W z@~?6FeIF6zr!KsF`}0T>@i%m^$Pf*p(P-mzgC@v!8*Ox;Mg#hr-oF|6ChyF5AJ>QP z{V_53|Mf5F%X|O8xn4fb|H@R3p7(YAd@%o>LBC;KJe-&P`qv-q=Raf&@&~9qjsxHQ z{GP-=k74`xMEUstd3HJ0S(c||eQZbXe}wmU4E+sWA^ql2mFLC$kx#<>`5l~_-|_Zu zxc-6qA5i@rrhj{N{D?mJMDjQos={p6X^VcIkH3>E%JKYbBe%5hliTP1)9K*UZ%gk_ zj(YrS;sEt3H)0TOG?Q1p$9?3MCs+>~hRNFY>`Vpf{vz#zFq1(=z7%SJs+rV@m|nIF zkM}ac+F&)M-gxhIt62$~(S)n38wvCX}FCxV&e6; z`)W%n0?$gf>~Z@xdf!|^ghE~s>@T0>iY`0>L_ik8Wj#8HB52!GvprCW`pXZRm~>yr zM)nQTBiKnB?*sHX z*%qEjidqZbZMEdr>N}9ML=ZZ)?j{%+QP0(7r_6Gnwq`&FG*u@%nnhaatMmItap(*3Ij%3Z6tu;k7B1C4R=RXO>9mVO>J^aIK`;41m)!Ke+e1>}=!v>>_5s?h+s}=J zIsGyZov?YjykFIy4m0hdRl4dFhwYMX)Zc-NM>J1dEPcC#8&|wGyMHDb>swDg>}qbg zANEl{1`4b?iZ*qxK;yUF2Vu*ya1D94jOeVZd;4J&vXh0S4hB89ep$Q@miD`c z6O20axK=d30juLU4zcupGFpLB8-q_gp`L+t07!}K$!rj41!v$*djrnmv3+&s0y%N=D(lD` zgT{%Y58-2{f2A3AgGS>?U9E7PvbjuOA#OUVAv0Qq+`48o^P#wKE;bB>dDG@|E01mK zDnFND$kzM{a4_ZnN*Fd$%5W%(m7X(N3PH)lYL9L>B%i$o%%yxy=xCVoQ4(N( zc`kA&JEX4hqs!$C`I$PZN4uFz$w=BT4SC82${t)mF0jj87InZ=d$?()w_^fSYuSt{ zWgkVuv`Lqv|o7Z*FS|H?c*+fp3*H|IV(jW+jO2Mtd<#AJcu+ zx$+$*MEY4LLN!eL>loNU~s(iG&d&V#K&)w}<)yty8a z6?}EMtZvA})1RHG8hIf(JNXrX?{Rl#*#Kk@ms+faF#egn0!=8KtfV!qz|CzW`Y3Zt(XCCi{TgDG3#ep%6wg*xDm3uK1-1^#+*$`wm4Y*HuJCn* zyu(;`$LHg66nw18y&5>3(-8$Gv?zbD^ZiKp2MZ%= zJq}LAm(}yT62mu{^WLjt!J;{7zH8bQJRaVQ;RKG?Cw;sqQ9F(^!%Bz;wK-`JJD%A=g=g+ZWJfi3T4^d%kp=YW3lxY?YR$ zgBeto*L7_y=o>|>J-1NTJ>JN*e4=Casmpk))r9aFfWu;sG;S)<$C?Y2ImY=0flXfR zNk<%CCIoZ4acTHgpBr@|?4B5P((o~J2-{3)vFo1_cn%v|61)nqGALWzD8a47yh#$u zsGfW3&OgC8E)1}Z{4sYB*usb-<)ZRJaPu@8c)*2|-w|8gQOA?O)uP z(5mh+$S~%tdEd@?Rs7y`boA5@ePY_#jApmy3VU`2B`jSqk6Wo%nH+9cjE*A7K^lwJ z5@%?V?(cZ0(f-423Ths-B2=)9pfl*yE*#4nn!v} z^q$o4)jm-Ngk=hX#NKuU3(C6^>#~=VkO6)V3Z2sPeV|j%J(q!wU%6}@qOv`VM4koU zK`LngT;CRpFgEs1spFTR2b^$da#YXLQbnJ|hjowb50_V8qo8cvx?AUB2wLd$b-rMCuW^gwcLSji_u>(lQWKzm>6xa7 z0UZsZn5109CqxXOjyBuj%5DQo`z>ei`HsBYt&lEK?RpaTXy3%|Vjo^M?qO%_w3dC5 z`cW+)9+bnA^J8E5u4}@yj>_>uo)G@+TpUe@d}pf7ddiSF zbj;(T?U0!L%wy+zzt2S2tkN~-(HPj&W&aq#&7-~CJvTOaG|ocGY{g|{Iewc|*tIwl zTRU%1x;JLMj>)ggO|2%{fG1to_Vlri`|%b1Is-9mU?cXl_f8>a@6qOoUuGJ5u&XQ^ zRcfOKna81f-nqqtuAduI7`eKy*3dr{1xwjlR~rnww=CYZW!z*2=n!-K`sN!)B>_+2iR9Tl($YiJUe!eko0EU*I8+C@@@mp8`$;n8nv+9Jaxyj4Q z6YuDl9dJ`s^T>N*Wdma=fr9(<4_!}pg5)@Hp`AT9z*0fVh*=>zK)$EiF-^4d3aO^4 zz2@uwXfZ$pj1ANoY@U3^t{zoqQ1(f*n(Y&(M#j+ zq&Orih8B6fJ*2W`I0cTg<>@jny08AZ$SCt%uPuHSED2wx5!N zke&p!r{wWVpCU?>X=mN?D|1Q6&^Ln?UfKb4i+_=`Y;ILTQajA>FFt6OXTY`CFSFgO zDE8$x*}7)xtZ;$uK(P~_jC{*?8Lz4dblwD3zAT_EZ9m}eJl}0LEqdLMnP6bts8LK0!b(edgRB)v$mC4l_R=hM@;hdCWclEOOee-k^rGUU{5`NN6=FC#@;1*T4J8+--s^M;E|t)0<~5Q47$4V+?&BLLx!{LuR>#HHdkKW8((0yVZvi>YT~n-wwYEVfHHcYOC+X4M zV|=Seu|a5S#FH*-4NjZ`j-&s_E}_ENT58WdG#y4~(IdWn5;wJxmp z(UqFb2eYoGZ*i-#xQ}G?){roA*ASg!RZ(QFp-u@LzKU0Fm5hv%22;gh!(z0aYl2Fk zR;$gg^_bH+64Gm`yx?^i;le_2xAz-e9X^Z#%+$HlgRtAj_xyb=;tFbL^UBejKyBb= zlosp&zrofwHZIymFYd@^i`zky@v5PJ@R;Y_;;5#LWq$5jOS};jTVK6TkmzGQqt@Yi zD44akOA}+|d1M=3)wb8{?D&O0&gF%#H_)u{Y9Ggz3Vh!WDQi4+w;b*RVLekiua3Uj zLV4{EtGlkTjxZ8KTOikC;pv;ynpJ(jsFwB>CT6zZVO=(EQhP%d^lS;Zy%t3ohnkz6 z3x4?-T*8Gq=#I`eYmFanuVpAz3c_<$zHnhs5-RNql4(_W5-AU^a@|I{i1@EX>$#nJ zu^=4|^U~Z8xY{*bH(#re503D#BcqlfQb}nGQKHrh)HkVsXQr@Na8CysA-&?Eba^c| zyw%^K=lgVpmTYI7bj=zFPv_@;_J?wo0x zFWtl7sZL%O(ZJAW?LDfCS?vaLtx$zJaEqI&yZK}BZrv9*>t&VB)6J9HOcK;!%_!bq zuKxSO?t|p{C_WljZUKS-*E44Q-8?QOnnP_$&2g^_TqdJlM*s)*uwyial~>3KJ?=e} z{OSC193q1O#TPVr@6`%D+bqDReke{`48-U=lH_^Y2F2$q-`yOLF}a&? 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