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This article mainly introduces how to use iTOL to add heat maps to the evolutionary tree, which is very detailed and has a certain reference value. Friends who are interested must read it!

The tool used is still the online software iTOL, but click here to draw a cool phylogenetic tree to learn how to use iTOL. The basic usage is no longer described, only the configuration file is described.

Profile preparation

First, let's take a look at the format of the required file:

DATASET_HEATMAP#SEPARATOR TABSEPARATOR SPACEDATASET_LABEL example_heatmapCOLOR # ff0000#define labels for each individual field columnFIELD_LABELS A1 A2 A3 B1 B2 B3MARGIN 0STRIP_WIDTH 25COLOR_MIN # ff0000COLOR_MAX # 0000ffUSE_MID_COLOR 1COLOR_MID # ffff00DATA155864 1.33118766397716 1.17857919899514-0.40955107083932-0.630306286554169-1.04604589954572-0.423863606028483334-0.05076910870376 1.3902493708319 1.06059120726857-0.886946484848482426725-0.693003965617928992 0.215479234585023 1.49464081584 0.68818558910058-1.21085219033218-0.76432470376 262626857-0.886948704782-0.820282432690725-0.693003965617928992 0.215479234585023 1.49464081584 0.68818558910058-1.21085219033218-0.76432470376 262626857-0.886948704782-0.820282432690725-0.693003965617928992 0.215479234585023 1.494681584 0.68818558910058-1.21085219033218-0.76432470376 .961867445609222 0.597829776500456 -0.461509960030431 -1.19966321785905 -0.964170542892806198215 0.96900544380798 1.21939609883181 0.426791627672821 -0.838548688929931 -0.653211840822719 -1.12343264055996623 0.727282455309188 1.17101033530621 0.806443403628944 -0.820220618604714 -0.920091135497558 -0.964424440142074209261 0.34017826857092 1.66855815466279 0.357643216125776 -0.545542360482732 -1.00245964906156 -0.818377629815193601 0.693183645180168 1.46683923827496 0.279576953582569 -1.04280232644501 -1.03511634861385 -0.36168116197883602 0.70273801067879 1.37079662629187 0.366781728164418 -0.773552511347515 -1.33593177597361 -0 .330832077813954229193 0.877365674482512 1.19322948550412 0.554384448895058-0.958849032442236-1.14266481591487-0.523465760524581

Format description:

The line starting with "#" in the configuration file is a comment line and is for illustrative purposes only, and iTOL does not read the contents of the line.

DATASET_HEATMAP: the profile data type declaration, which declares that the dataset adds heat map information to the evolutionary tree.

SEPARATOR SPACE: specifies the data delimiter, that is, data columns are separated by spaces.

COLOR # ff00ff: specifies the initial color of the dataset, which can be changed later.

FIELD_LABELS A1 A2 A3 B1 B2 B3: define a label for each column of data in DATA (specify the sample name).

MARGIN 0: specifies the distance between the heat map and the evolutionary tree, which can be negative, resulting in overlap with the evolutionary tree.

STRIP_WIDTH 25: specify the width of each grid in the heat map.

COLOR_MIN # ff0000: specifies the color of the minimum value in the heat map.

COLOR_MAX # 0000ff: specifies the color of the maximum value in the heat map.

USE_MID_COLOR 1: specifies whether to set the intermediate value color, 0 for no setting and 1 for setting.

COLOR_MID # ffff00: specifies the color of the intermediate value in the heat map.

If there are no special settings, the above part usually does not need to be changed, just copy it and use it.

The line after DATA is the expression data of all genes in each sample. The data I use here is the value of gene expression level log2 (FPKM) after normalized conversion (scale number) in the sample. The data are divided into seven columns, the first is the evolutionary branch node ID (gene ID), and the second to the seventh is the data of gene expression in each sample. Note that the data should be consistent with the number and order of the sample names specified by FIELD_LABELS.

Comment file beautification

After preparing the comment file according to the above format, drag it directly to the location where the iTOL evolutionary tree is displayed, and you can automatically add a heat map to the evolutionary tree. If you are not satisfied with the effect of the picture, you can also adjust the color, width and position of the heat map in Datasets.

The above is all the content of the article "how to use iTOL to add heat maps to the evolutionary tree". Thank you for reading! Hope to share the content to help you, more related knowledge, welcome to follow the industry information channel!

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