From 49da41ebbe66284a3aff78677b750fb1187da18f Mon Sep 17 00:00:00 2001 From: shang-hongyun Date: Thu, 24 Oct 2024 17:14:35 +0800 Subject: [PATCH 1/4] fixreadme --- README.md | 98 ++++++++++++++++++++++++++++++++----------------------- 1 file changed, 57 insertions(+), 41 deletions(-) diff --git a/README.md b/README.md index f249b3f..9740cc2 100644 --- a/README.md +++ b/README.md @@ -1,12 +1,19 @@ ### Introduction ### -We defined the ILS/IH index to represent the degree of Incomplete lineage sorting (ILS) and introgression (IH) among lineages. This tool can quickly detect and visualize ILS/IH index between lineages of tree results run by ASTRAL option -u 2 or -t -2, with short running time, helping users to preliminatively determine ILS and IH and screen lineages for further analysis.For more details of ILS/IH index, please see https://www.biorxiv.org/content/10.1101/2024.09.02.610893v1. Executable version for Windows and Linux can be downloaded at https://figshare.com/articles/dataset/phytop_executable_versions_in_windows_and_linux/27276699 +We defined the ILS/IH index to represent the degree of Incomplete lineage sorting (ILS) and introgression (IH) among lineages. This tool can quickly detect and visualize ILS/IH index between lineages of tree results run by ASTRAL option -u 2 or -t -2, with short running time, helping users to preliminatively determine ILS and IH and screen lineages for further analysis.For more details of ILS/IH index, please see https://www.biorxiv.org/content/10.1101/2024.09.02.610893v1. Any nodes of phylogenetic tree can be regarded as consisting of two sister groups and one outgroup, and these three lineages can form three topologies q1, q2, q3 (as shown in the figure below),The topology with the highest proportion is denoted as q1. ILS/IH index is calculated based on the number and proportion of these topologies. ![q123](example_data/legend_forintroduce/q123.png) **Figure. The three topological structures of gene trees** Any combination of three lineages produces three topologies, When the ILS index is at its maximum of 100% and there is no IH, we expect q1 = q2 = q3 = 100%/3. When the IH index reaches 50% and there is no ILS, q1 = q2 = 50% is expected. ### Quick install and start ### -Download and install Phytop: +Executable version for Windows and Linux can be downloaded at https://figshare.com/articles/dataset/phytop_executable_versions_in_windows_and_linux/27276699 +``` +# run help for the executable version for Windows +phytop.exe -h +# run help for the executable version for Linux +phytop_linux -h +``` +Download and install Phytop in Linux: ``` git clone https://github.com/zhangrengang/phytop cd phytop @@ -118,80 +125,89 @@ Output: Temporary directory [default=tmp] ``` -Get barcharts with collapse for clades: +Visual parameters for adjusting graph output: +1.Get barcharts with different colors: ``` -phytop astral.tree -clades setcladefile -collapse +phytop astral.tree -colors red,yellow,black ``` -![pie](example_data/legend_forintroduce/astral.tree.bar.collepse-1.png) -**Figure. Visual result of Phytop on example data with collapse for clades.** Juglans regia and Juglans sigillata were collepse for Juglans1 +![pie](example_data/legend_forintroduce/astral.tree-colors-red,yellow,black-1.png) +**Figure. Visual result of Phytop on example data with "-colors" parameter.** Set the columns to different colors -Get barcharts with different colors: +2.Resize barplot and text ``` -phytop sog.sc.cds.mm0.5.genetrees.astral -colors 'red','yellow','black' +phytop astral.tree -figsize 1 -fontsize 4 ``` -![pie](example_data/legend_forintroduce/astral.tree-colors-red,yellow,black-1.png) -**Figure. Visual result of Phytop on example data with "-colors" parameter.** Set the columns to different colors +![pie](example_data/legend_forintroduce/astral.tree-figsize1-fontsize4-1.png) +**Figure. Visual result of Phytop on example data with "-figsize" and "-fontsize" parameters. "-figsize 1 -fontsize 4" in this example.** These parameters can be used to adjust the image size and font size of the barplots. -Get barcharts displays a selection of nodes: +3.Get piecharts: ``` -phytop astral.tree -clades setcladefile -onshow Juglans1 +phytop astral.tree -pie -cp ``` -![pie](example_data/legend_forintroduce/astral.tree.bar.onshow-1.png) -**Figure. Visual result of Phytop on example data with a subset of nodes.** Only the information about the specified node is displayed +![pie](example_data/legend_forintroduce/astral.tree.pie-1.png) +**Figure. Visual result of Phytop on example data with "-pie -cp" parameters.** In the pie chart, only the proportions of the q1 topologies are shown -Get barcharts displays a selection of nodes: +4.Resize the pieplot size ``` -phytop astral.tree -clades setcladefile -noshow Juglans1 +phytop astral.tree -pie -pie_size 20 ``` -![pie](example_data/legend_forintroduce/astral.tree.bar.noshow-1.png) -**Figure. Visual result of Phytop on example data with specified node information not displayed.** The information about the specified node is not displayed +![pie](example_data/legend_forintroduce/astral.tree-pie-pie_size20-1.png) +**Figure. Visual result of Phytop on example data with "-pie_size". "-pie -pie_size 20" in this example.** This parameter can be used to adjust font size of of piecharts. -Get piecharts: +5.Get barcharts with collapse for clades: ``` -phytop astral.tree -pie -cp +phytop astral.tree -clades setcladefile -collapse ``` -![pie](example_data/legend_forintroduce/astral.tree.pie-1.png) -**Figure. Visual result of Phytop on example data with "-pie -cp" parameters.** In the pie chart, only the proportions of the q1 topologies are shown +![pie](example_data/legend_forintroduce/astral.tree.bar.collepse-1.png) +**Figure. Visual result of Phytop on example data with collapse for clades.** Juglans regia and Juglans sigillata were collepse for Juglans1 -Customizing the visualization output: +6.Get barcharts displays a selection of nodes: ``` -phytop astral.tree -align +phytop astral.tree -clades setcladefile -onshow Juglans1 ``` -![pie](example_data/legend_forintroduce/astral.tree_align-1.png) -**Figure. Visual result of Phytop on example data with "-align" parameter.** This parameter can be used to make leaf names aligned. +![pie](example_data/legend_forintroduce/astral.tree.bar.onshow-1.png) +**Figure. Visual result of Phytop on example data with a subset of nodes.** Only the information about the specified node is displayed +7.Get barcharts displays a selection of nodes: ``` -phytop astral.tree -subset Juglans_nigra Juglans_sigillata Juglans_regia +phytop astral.tree -clades setcladefile -noshow Juglans1 ``` -![pie](example_data/legend_forintroduce/astral.tree-subset_Juglans_nigraJuglans_sigillataJuglans_regia-1.png) -**Figure. Visual result of Phytop on example data with "-branchsize" parameter. "-branchsize 20" in this example.** This parameter can be used to select subset of leaves. +![pie](example_data/legend_forintroduce/astral.tree.bar.noshow-1.png) +**Figure. Visual result of Phytop on example data with specified node information not displayed.** The information about the specified node is not displayed + +Visual parameters for adjusting fonts +1.Adjust the leaf size +``` +phytop astral.tree -leaf_size 20 +``` +![pie](example_data/legend_forintroduce/astral.tree-leaf_size20-1.png) +**Figure. Visual result of Phytop on example data with "-leaf_size". "-leaf_size 20" in this example.** This parameter can be used to adjust font size of font size of leaf names. +2.Adjust the font size of branch size ``` phytop astral.tree -branch_size 20 ``` ![pie](example_data/legend_forintroduce/astral.tree_branchsize20-1.png) **Figure. Visual result of Phytop on example data with "-branch_size" parameter. "-branch_size 20" in this example.** This parameter can be used to adjust font size of text in branch. +3.Make barplot not display text ``` phytop astral.tree -notext ``` ![pie](example_data/legend_forintroduce/astral.tree_notext-1.png) **Figure. Visual result of Phytop on example data with "-notext" parameter.** Use this parameter to make the text of the barplots not display. +Visual parameters for adjusting clades: +1.Customizing the location of lineages: ``` -phytop astral.tree -figsize 1 -fontsize 4 -``` -![pie](example_data/legend_forintroduce/astral.tree-figsize1-fontsize4-1.png) -**Figure. Visual result of Phytop on example data with "-figsize" and "-fontsize" parameters. "-figsize 1 -fontsize 4" in this example.** These parameters can be used to adjust the image size and font size of the barplots. - -``` -phytop astral.tree -leaf_size 20 +phytop astral.tree -align ``` -![pie](example_data/legend_forintroduce/astral.tree-leaf_size20-1.png) -**Figure. Visual result of Phytop on example data with "-leaf_size". "-leaf_size 20" in this example.** This parameter can be used to adjust font size of font size of leaf names. +![pie](example_data/legend_forintroduce/astral.tree_align-1.png) +**Figure. Visual result of Phytop on example data with "-align" parameter.** This parameter can be used to make leaf names aligned. +2.Select part of the lineages to show ``` -phytop astral.tree -pie -pie_size 20 +phytop astral.tree -subset Juglans_nigra Juglans_sigillata Juglans_regia ``` -![pie](example_data/legend_forintroduce/astral.tree-pie-pie_size20-1.png) -**Figure. Visual result of Phytop on example data with "-pie_size". "-pie -pie_size 20" in this example.** This parameter can be used to adjust font size of of piecharts. +![pie](example_data/legend_forintroduce/astral.tree-subset_Juglans_nigraJuglans_sigillataJuglans_regia-1.png) +**Figure. Visual result of Phytop on example data with "-branchsize" parameter. "-branchsize 20" in this example.** This parameter can be used to select subset of leaves. \ No newline at end of file From 6bb3b7f3ad9b28aae2dc6002fb0884d7668e3e5d Mon Sep 17 00:00:00 2001 From: shang-hongyun Date: Thu, 24 Oct 2024 17:17:19 +0800 Subject: [PATCH 2/4] fixreadme --- README.md | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index 9740cc2..680fef6 100644 --- a/README.md +++ b/README.md @@ -126,6 +126,7 @@ Output: ``` Visual parameters for adjusting graph output: + 1.Get barcharts with different colors: ``` phytop astral.tree -colors red,yellow,black @@ -175,7 +176,8 @@ phytop astral.tree -clades setcladefile -noshow Juglans1 ![pie](example_data/legend_forintroduce/astral.tree.bar.noshow-1.png) **Figure. Visual result of Phytop on example data with specified node information not displayed.** The information about the specified node is not displayed -Visual parameters for adjusting fonts +Visual parameters for adjusting fonts: + 1.Adjust the leaf size ``` phytop astral.tree -leaf_size 20 @@ -198,6 +200,7 @@ phytop astral.tree -notext **Figure. Visual result of Phytop on example data with "-notext" parameter.** Use this parameter to make the text of the barplots not display. Visual parameters for adjusting clades: + 1.Customizing the location of lineages: ``` phytop astral.tree -align From d05087e392933d1f802d453628536284f00ae235 Mon Sep 17 00:00:00 2001 From: shang-hongyun Date: Thu, 24 Oct 2024 17:18:48 +0800 Subject: [PATCH 3/4] fixreadme --- README.md | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/README.md b/README.md index 680fef6..ee3e6b0 100644 --- a/README.md +++ b/README.md @@ -127,14 +127,14 @@ Output: Visual parameters for adjusting graph output: -1.Get barcharts with different colors: +1\. Get barcharts with different colors: ``` phytop astral.tree -colors red,yellow,black ``` ![pie](example_data/legend_forintroduce/astral.tree-colors-red,yellow,black-1.png) **Figure. Visual result of Phytop on example data with "-colors" parameter.** Set the columns to different colors -2.Resize barplot and text +2.Resize barplot and text: ``` phytop astral.tree -figsize 1 -fontsize 4 ``` @@ -148,7 +148,7 @@ phytop astral.tree -pie -cp ![pie](example_data/legend_forintroduce/astral.tree.pie-1.png) **Figure. Visual result of Phytop on example data with "-pie -cp" parameters.** In the pie chart, only the proportions of the q1 topologies are shown -4.Resize the pieplot size +4.Resize the pieplot size: ``` phytop astral.tree -pie -pie_size 20 ``` @@ -178,21 +178,21 @@ phytop astral.tree -clades setcladefile -noshow Juglans1 Visual parameters for adjusting fonts: -1.Adjust the leaf size +1.Adjust the leaf size: ``` phytop astral.tree -leaf_size 20 ``` ![pie](example_data/legend_forintroduce/astral.tree-leaf_size20-1.png) **Figure. Visual result of Phytop on example data with "-leaf_size". "-leaf_size 20" in this example.** This parameter can be used to adjust font size of font size of leaf names. -2.Adjust the font size of branch size +2.Adjust the font size of branch size: ``` phytop astral.tree -branch_size 20 ``` ![pie](example_data/legend_forintroduce/astral.tree_branchsize20-1.png) **Figure. Visual result of Phytop on example data with "-branch_size" parameter. "-branch_size 20" in this example.** This parameter can be used to adjust font size of text in branch. -3.Make barplot not display text +3.Make barplot not display text: ``` phytop astral.tree -notext ``` @@ -208,7 +208,7 @@ phytop astral.tree -align ![pie](example_data/legend_forintroduce/astral.tree_align-1.png) **Figure. Visual result of Phytop on example data with "-align" parameter.** This parameter can be used to make leaf names aligned. -2.Select part of the lineages to show +2.Select part of the lineages to show: ``` phytop astral.tree -subset Juglans_nigra Juglans_sigillata Juglans_regia ``` From 7af3a31ece6eb4e497f342a36fcf46f2b75fa552 Mon Sep 17 00:00:00 2001 From: shang-hongyun Date: Thu, 24 Oct 2024 17:20:01 +0800 Subject: [PATCH 4/4] fixreadme --- README.md | 22 +++++++++++----------- 1 file changed, 11 insertions(+), 11 deletions(-) diff --git a/README.md b/README.md index ee3e6b0..34e546c 100644 --- a/README.md +++ b/README.md @@ -134,42 +134,42 @@ phytop astral.tree -colors red,yellow,black ![pie](example_data/legend_forintroduce/astral.tree-colors-red,yellow,black-1.png) **Figure. Visual result of Phytop on example data with "-colors" parameter.** Set the columns to different colors -2.Resize barplot and text: +2\. Resize barplot and text: ``` phytop astral.tree -figsize 1 -fontsize 4 ``` ![pie](example_data/legend_forintroduce/astral.tree-figsize1-fontsize4-1.png) **Figure. Visual result of Phytop on example data with "-figsize" and "-fontsize" parameters. "-figsize 1 -fontsize 4" in this example.** These parameters can be used to adjust the image size and font size of the barplots. -3.Get piecharts: +3\. Get piecharts: ``` phytop astral.tree -pie -cp ``` ![pie](example_data/legend_forintroduce/astral.tree.pie-1.png) **Figure. Visual result of Phytop on example data with "-pie -cp" parameters.** In the pie chart, only the proportions of the q1 topologies are shown -4.Resize the pieplot size: +4\. Resize the pieplot size: ``` phytop astral.tree -pie -pie_size 20 ``` ![pie](example_data/legend_forintroduce/astral.tree-pie-pie_size20-1.png) **Figure. Visual result of Phytop on example data with "-pie_size". "-pie -pie_size 20" in this example.** This parameter can be used to adjust font size of of piecharts. -5.Get barcharts with collapse for clades: +5\. Get barcharts with collapse for clades: ``` phytop astral.tree -clades setcladefile -collapse ``` ![pie](example_data/legend_forintroduce/astral.tree.bar.collepse-1.png) **Figure. Visual result of Phytop on example data with collapse for clades.** Juglans regia and Juglans sigillata were collepse for Juglans1 -6.Get barcharts displays a selection of nodes: +6\. Get barcharts displays a selection of nodes: ``` phytop astral.tree -clades setcladefile -onshow Juglans1 ``` ![pie](example_data/legend_forintroduce/astral.tree.bar.onshow-1.png) **Figure. Visual result of Phytop on example data with a subset of nodes.** Only the information about the specified node is displayed -7.Get barcharts displays a selection of nodes: +7\. Get barcharts displays a selection of nodes: ``` phytop astral.tree -clades setcladefile -noshow Juglans1 ``` @@ -178,21 +178,21 @@ phytop astral.tree -clades setcladefile -noshow Juglans1 Visual parameters for adjusting fonts: -1.Adjust the leaf size: +1\. Adjust the leaf size: ``` phytop astral.tree -leaf_size 20 ``` ![pie](example_data/legend_forintroduce/astral.tree-leaf_size20-1.png) **Figure. Visual result of Phytop on example data with "-leaf_size". "-leaf_size 20" in this example.** This parameter can be used to adjust font size of font size of leaf names. -2.Adjust the font size of branch size: +2\. Adjust the font size of branch size: ``` phytop astral.tree -branch_size 20 ``` ![pie](example_data/legend_forintroduce/astral.tree_branchsize20-1.png) **Figure. Visual result of Phytop on example data with "-branch_size" parameter. "-branch_size 20" in this example.** This parameter can be used to adjust font size of text in branch. -3.Make barplot not display text: +3\. Make barplot not display text: ``` phytop astral.tree -notext ``` @@ -201,14 +201,14 @@ phytop astral.tree -notext Visual parameters for adjusting clades: -1.Customizing the location of lineages: +1\. Customizing the location of lineages: ``` phytop astral.tree -align ``` ![pie](example_data/legend_forintroduce/astral.tree_align-1.png) **Figure. Visual result of Phytop on example data with "-align" parameter.** This parameter can be used to make leaf names aligned. -2.Select part of the lineages to show: +2\. Select part of the lineages to show: ``` phytop astral.tree -subset Juglans_nigra Juglans_sigillata Juglans_regia ```