From d455fad79f78611f8ff7deaa731517be7ecdd448 Mon Sep 17 00:00:00 2001 From: anderska57 Date: Wed, 13 May 2026 15:16:55 -0400 Subject: [PATCH 1/2] Updated post-phyloseq flow chart --- .DS_Store | Bin 6148 -> 6148 bytes docs/processing.md | 16 ++++++++++------ 2 files changed, 10 insertions(+), 6 deletions(-) diff --git a/.DS_Store b/.DS_Store index 027b0bc2983264d89c1b5ca778dab9272b10669a..570c1275b7fad57b66ba154af04e4865de61f3b2 100644 GIT binary patch delta 67 zcmZoMXfc=|#>B)qu~2NHo+2ab#(>?7jI5h^SfUv>i*X3DOl;`i%+A5j0aUVCkmEb^ VWPTAx4hA4#WME*~93irX82~Rb4*&oF delta 260 zcmZoMXfc=|#>B!ku~2NHo+2a1#(>?7iyN4k7&$icFhw&4axxS#q%x!dF^JA%NM=a& z%*jtq%E?b+U|S{v^V;u!UbBkIX zg=#}1Qy|CO)U>vilS5Ql-#REhJ0~|UzZ+~I10y4ZX5fX=FscX0z+zola8X`PeqK6I mmT_ZY3FBsV4t@@xA2$~=e`lV|FXG4nG>{2o$mR%^SoP diff --git a/docs/processing.md b/docs/processing.md index d36fbb4..7dda591 100644 --- a/docs/processing.md +++ b/docs/processing.md @@ -1,12 +1,16 @@ # Overview -After creating a phyloseq object, lab members have developed the below workflow for beginning to process and analyze it. The rest of the pages in this section will walk you though the three steps of calculating diversity metrics and relative abundance and creating a PCA plot: +Once a phyloseq object is created, the following workflow may be used as a template for further processing and beginning analysis. The rest of the pages in this section will expand on the details of each step. ``` mermaid graph TD - A[Unfiltered Phyloseq] -->|Step 1: Review/BLAST NAs, add taxonomic assignments for any that should be kept| B[Unfiltered Phyloseq with Added Taxonomic Assignments for Select NAs] - B -->|Step 2: Filter out remaining NAs & human reads for 12Sv5| C[Filtered Phyloseq] - C -->|Steps 3: Calculate diversity metrics and add to sample metadata| D[Filtered Phyloseq + Diversity Metrics] - D -->|Step 4: Perform CLR transform on relative abundances| E[CLR-Transformed Phyloseq] - E -->|Step 5: Create PCA biplot| F[PCA Biplot] + A[Unfiltered Phyloseq] -->|Step 1: Assign Common Names| B[Phyloseq with Common Name Assignments] + B -->|Step 2: Review Unassigned Taxa - NAs| C[Phyloseq with Updated Assignments for Select NAs] + C -->|Step 3: Taxa Filtering| D[Phyloseq with Filtered Taxa] + D -->|Step 4: Sample Filtering| E[Phyloseq with Filtered Samples] + E -->|Step 5: Prune Taxa| F[Phyloseq with Pruned Taxa after Sample Filtering] + F -->|Step 6: Taxa Glomming| G[Phyloseq with Glommed Taxa] + G -->|Step 7: Calculate Diversity Metrics| H[Phyloseq with Diversity Metrics] + H -->|Step 8: Calculate Relative Abundances and CLR-Transform| I[CLR-Transformed Phyloseq] + I -->|Step 9: Perform PCA| J[PCA Biplot] ``` \ No newline at end of file From 6d8fedcba5ea53278ce9e5c407ca331d0bc0e157 Mon Sep 17 00:00:00 2001 From: anderska57 Date: Wed, 13 May 2026 15:35:57 -0400 Subject: [PATCH 2/2] add DS_Store to gitignore --- .DS_Store | Bin 6148 -> 0 bytes .gitignore | 1 + docs/.DS_Store | Bin 8196 -> 0 bytes 3 files changed, 1 insertion(+) delete mode 100644 .DS_Store delete mode 100644 docs/.DS_Store diff --git a/.DS_Store b/.DS_Store deleted file mode 100644 index 570c1275b7fad57b66ba154af04e4865de61f3b2..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 6148 zcmeHKO;6iE5SgF zKk46T-|TK8KCd*YW~AA-Gdr{PzO{BeM5Nl|q)AjGA`i+~@zJ~@JkI(;D$cVCR6NJm zO!wnV$FO-qk>zKA_pV9_Y3ft)Z2!JsZ10Z|vyeqxJSnc-KL3iZv$PmB8oyO#rMkMd z?s?v(cOL!JlW5c%jf-|~c*@pyt+ROE@5RUIVA8E^9qN44OY_0dB&5jzA!jFPp6E$i zkMpE3xse_4eBbZZcBa#2J!l@ZX7ym&Y&BZ-;9!4$HuJsh-A|vtbuY84T;Eyd6+TNN z9~{o%9-YNl2m`{v zQZnEUM{jc}-%egi7!U^jB?Eju1W?A%VQJAE9cWAm0Ib4o1by@C4-D7=3>}sh;ejZd z3bd)pl^DuZ4$7uuJaqA;MVn5_JQ?%2Co5N>C|7u>z=V?uElMj42m? z>;I=oVhIDnz<x;$lT^m4uKv_7hw75t?$6UpT<*WE3)Cl|mcYvY8 T(jq(%`4KQQNFxlqD+7N4=VfQ2 diff --git a/.gitignore b/.gitignore index 308b0a8..99f8932 100644 --- a/.gitignore +++ b/.gitignore @@ -1,2 +1,3 @@ # Local reference materials (not part of the site) reference/ +.DS_Store diff --git a/docs/.DS_Store b/docs/.DS_Store deleted file mode 100644 index 3bf18e149350a40e41ddefcd3e42eddc1091bf2a..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 8196 zcmeHM&u<$=6n^6bv#y=SGzn>upq8vkJ)|X8l;+R_t`k&691_)0N!1@_*E?~Rtar@r z+G!d^@)deT;syu)0N})5fH-o33xYc*xB(~lW@g=PHtVWLm8jaCXy!f7e&4+Do0<1K z8zN$jzFi|aOGE~$l;t9tlp>$YdZOf_o^y~4e4;Md>#k^9uCPv^vyRLInFlftWFE*o zka^&F@BnhQEXJ6;ub*aZ=7G!uFQo@$e5jyGS&!sUOBFiMs4D>EB)V0Bj(dROR3cfA z85ql;rp%f?5glW)A6{k2#(DG zx%0l`*hkb zd;(vj58?O$YJi3JVXcQ{OD@7!308?*Ff6*HHU|eo&a#u_u{WQV_hKyMShqOsL9|cV zr=xxP>u8@AP8Ca2r>D!WO`n;bnVFq?eSZF2t2|?w?Y)jK_ui^-h2L=d{C3B8>}Jnw zJ6>lytcSe2 z?(GPSKfoE;=!K5(f}7kAAa9wzZ+acxIJoPY7I!zih6qE^ZI!1Lw=KL)pG)4h16|Iu z`pzHN4Jg(6dn4tdR?1Y>3ikW#NQ)%f+QTU<6sq;jsK=lSbd|2tCJseN59u@dlD?+z z=m+|Rey6_}W2e{*n`3XW^K6kVvny;xGjpRu_{MP?>ZixpwR1bQW?OW7G0s?QSFEi? z@yIy*^S9>DUwkj)*Awvef5P{6pMEZhK$6G7ZsX9V