From 878df7df53da7e8a3cbf75677541395965825835 Mon Sep 17 00:00:00 2001 From: "flo.minion.info@gmail.com" Date: Tue, 27 Apr 2021 11:10:24 +0200 Subject: [PATCH] Changes to README --- README.md | 10 +++++++--- 1 file changed, 7 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index 806f526..5a885db 100644 --- a/README.md +++ b/README.md @@ -143,6 +143,7 @@ Example 3: | :-------------: |:-------------:| | | | +**Figure 1. CV distributions of A: test/broad_peaks/, B: test/sharp_peaks.** The diagram will give you a first impression of the binding specificity of your protein of interest. The diagram also tells you about the performance/quality of your experiment. An experiment with lots of unspecific binding sites will have @@ -156,6 +157,7 @@ in our example B. | :-------------: |:-------------:| | | | +**Figure 2. Normalized CV distributions of A: test/broad_peaks/, B: test/sharp_peaks.** The normalized CV distribution helps to identify specific and unspecific sites within an experiment. The normalized CV is in a range [0,1]. A specific site will have a value of 1. An unspecific site will have a value of 0. @@ -193,9 +195,8 @@ You will get some plots for the classification, saved in the folder `clustering_ | :-------------: |:-------------:| | | | -If you turned on the smoothing you will get four types of cluster sets. The first one shows you -some example raw peak profiles assigned to the specific cluster (e.g. cluster_1.pdf -for cluster 1; Figure A). The second one shows you some example smoothed and sometimes translocated peak profiles to the specific cluster (e.g. cluster_smoothed1.pdf for cluster 1; Figure B). Profile like figure B are used for the classification. The profiles are colored based on the clusters as seen as in the uMAP plot. +**Figure 3. Example cluster profile for data test/mixed_peaks/; Cluster 3 A: raw profile, B: smoothed profile.** +If you turned on the smoothing you will get four types of cluster sets. The first one shows you some example raw peak profiles assigned to the specific cluster (e.g. cluster_3.pdf for cluster 3; Figure A). The second one shows you some example smoothed and sometimes translocated peak profiles to the specific cluster (e.g. cluster_smoothed3.pdf for cluster 3; Figure B). Profile like figure B are used for the classification. The profiles are colored based on the clusters as seen as in the uMAP plot. ### Overview Cluster Profiles (pdf) @@ -207,11 +208,13 @@ for cluster 1; Figure A). The second one shows you some example smoothed and som | :-------------: | | | +**Figure 4. Cluster profile summary for data test/mixed_peaks/.** The third one is an example profile, such as Figure A for each cluster in one plot (overview_cluster.pdf; Figure C). The fourth one are the average profiles of each cluster (e.g. cluster_average_profiles.pdf; Figure D). ### k-means Optimization +**Figure 5. Kmeans optimization for data test/mixed_peaks/.** The plot `kmeans_Optimization.pdf` shows you the optimization scheme. If you data has a very low complexity, that is to say, you have lots of similar peak profiles, then the percent of variance explained will be very low (second plot). It is also @@ -221,6 +224,7 @@ peak profiles, as in our example, then the variance explained will be `> 90%`. ### uMAP Plot +**Figure 6. uMAP plot for data test/mixed_peaks/.** The plot `uMAP.pdf` shows you the data in the new dimension found by the uMAP dimensional reduction algorithm. In correspondance to the the k-means optimization, highly distinguishable peaks will appear in the plot as very clearly separated