mountain

Mountain plot

Mountain plot, created by Dr. Adi Gazdar and Dr. Kai Song, is a very useful scatter plot for visualizing and analyzing genome-wide variations of copy numbers [1, 2]. It gains its name from the similarity of such a plot to the ups and downs of mountains outlines seen from afar. In Mountain plot, each spot is the median/mean value of concern data types (i.e. copy number etc.) of each gene in a group which can be a batch or a cancer type. The genes are sorted according to their locations. The space between two arms of each chromosome is the location of the corresponding centromere.

Originally, Mountain plot was used to analyze genome-wide variations of copy numbers. Due to the wonderful visualizing effect, we provide Mountain plot for mRNA expression and methylation values.

Because it is used to visualize the variations of copy numbers or other data types, the values of corresponding non-malignant samples are plotted in default if they are available for the given cancer types. When more than one cancer types are specified, all available non-malignant samples of all these cancer types will be combined in one group which means only one spot for each gene in all non-malignant samples from different specified cancer types.

As we mentioned above, there are three ways to get into the Mountain plot page.

→ Through the Navigation bar at the Home page, select “Mountain plot” under “Data Analysis”;

→ Go to “Data Analysis” page, then go to “Data visualization” area, select “Mountain plot”;

→ Through the link in the “Link area” at the Home page, go to “Data Analysis” page, then go to “Data visualization” area, select “Mountain plot”.

For “Mountain plot” page, there are five areas:

→ Navigation bar: You can switch to other pages through this navigation bar.

→ Setting area: You can specify genes, cancer types, data types, cutoff values and other parameter details here.

→ Plotting area: The Mountain plot will be plotted in this area.

→ Figure Downloading and DIY area: You can download Mountain plot in certain format and size. You can also customize line color, line shape, marker color, marker shapes through the option buttons in this area.

→ Link area: Necessary links are available for you to switch to other pages or websites.

Note: quick help can be available through putting your mouse on the small question marks besides certain options in this pages.

1. It reminds you which kind of plot you are working on.

2. You can select mRNA expression, copy number variation. Originally, Mountain plot was used to visualize genome copy number variations. But we expand it to visualize mRNA expression, methylation, and so on.

3. You can a select concern cancer type through the drop-down cancer list here.

In TCGA/GDC dataset, non-malignant samples and tumor samples are not both always available for all cancer types. Available sample types vary for different data type even for the same cancer type. For example, for acute myeloid leukemia (LAML) cancer, no non-malignant samples of mRNA expression values are available, but both non-malignant and tumor samples are available for copy number variation data. Different legends are added before cancer names to tell you which kind of samples of the given cancer types can be available.

Note: The gene copy numbers in non-malignant samples are supposed to be 2. But because of so many reasons, they are a little bit different from 2. To make a good comparison, all non-malignant samples are combined together as a super-control. You can select it by selecting “[all-non-malignant]” at the bottom of the cancer list.

⚠: without non-malignant which means only tumor samples of this cancer type are available for the data type specified in (2).

❌: not available which means neither tumor samples nor non-malignant samples of this cancer type are available for the data type specified in (2).

In the plotting area, *_T is used as symbols of groups of tumor samples;

4. You can select a concern chromosome through the drop-down list here. Now only 1-22 chromosomes are available.

5. You can specify concern gene here by inputting gene symbols. Only HUGO (Human Genome Organization) symbols are accepted. For example: EGFR, KRAS, TP63…. If you want to input more than one gene symbols, a common and a space should be used to separate two gene symbols.

Note: small case and big case are all acceptable. For example, kRAS, kras, KRas, KRAS are all treated as the same gene.

6. In Mountain plot, each spot can be median or mean values of each group. You can specific either one of them through this drop-down list.

7. You can specify concern transformation type, whether plot cytoband information or not by checking the small boxes before each of them. Log: after checking this option, log transformation will be applied to the data before Bee-swarm plot (for mRNA expression values, it's log2 transformation; for CNV (copy number variation) values, it's log2(CNV/2) transformation).

8. You can input cutoff values here to see whether the median/mean values of each group are above or below them.

After setting all these necessary options, click “GO” button at the bottom of this area, the Mountain plot will be created in the plotting area. There are no limits on how many cancer types you want to plot. But due to the configuration of your computer, the internet speed and the data sizes need to be transmitted for plotting (several times of the sample sizes), it may take a while to transmit and load the data for plotting. The more cancer types you want to plot, the longer the response time will it need.

Mountain plot figures will be shown in this area.

A toolbar will show up at the top right of this plotting area when a Mountain plot is created.

1. Zoom in: Rectangular zoom in tool. This tool allows you to select a region to display at full application size. After clicking this botton, your mouse will turn into a small cross. Then click and hold the left mouse button and drag a rectangle around a portion of the screen and have it zoom in.

2. Zoom out: Zoom back to the status you have up step by cliking it.

3. Restore: Show the plots in the original portion.

4. Save as Image: You can click it to swich into a image saving webpage then click right mouse button to save this image. You also can specify the image format and size by selecting the options in the Figure downloading and DIY area.

5. Data table: If you want to download the sample data in a table, you can click this button.

Then a table containing all data will show up in the plotting area like this: The first part of this table shows the similiarity scores of different groups to the non-maglinant_median/ non-maglinant_mean group. Please go to the Introduction of curve similiarity to see the details. Then the value and sample ID of each individual case in each group. You can select and copy the whole table or any part of it into a word or excel file by selecting and clicking right mouse button as you usally do.

You can scroll down to see the information of other samples. You also can click the “close” button at the bottom left of this page to close the table page and go back to the default page with the plotting area.

There are two more ways to zoom in:

♦ Vertically zoom in: There is a 'zoom bar' at the right edge of the plotting area. Click and hold on either one of the two buttons on it, you can zoom in or zoom out vertically.

♦ Horizontally zoom in: Slide the mouse wheel (for apple magic mouse, slide up or down) up or down, you can zoom in or zoom out horizontally.

For your convinence, the sample ID and other details of each individual sample will show up when you put your mouse on the corresponding marker.

For example: in the above figure, aftering putting the mouse on a marker, a catalog showed up is:

→ First row: the group message of this sample;

→ Second row: x-axis, y-axis, sample ID

♦ x-axis: start location of the concern gene in the corresponding chromosome;

♦ y-axis: median/mean mRNA expression, copy number variation values depends on which data type you are working on;

♦ gene symbol: HUGO (Human Genome Organization) symbols are used here.

Therefore, in this example: the gene symbol is SEC61G, its start location in chromosome 7 is 54819939 and the mean value of its copy number variations in Glioblastoma multiforme is 7.2875.

You can specify image format (png or jpg) and size/dimensions for the image to download.

You can modify colors, shapes and other details of this figure for you own style.

Y-Limits: To make it easier for comparison by using the same Y-axis limits in the Mountain plots for different chromosomes, you can specify Y-axis limits here. Only the limits broader than the default ones are acceptable. (You can use the zoom bar mentioned above to make the limits narrower.)

Select the group whose style you want to modify, then modify the color, shape of the markers, box, static lines here.

Example 1: Plotting Mountain plot of mean values of copy numbers on chromosome 7 of glioblastoma multiforme tumor and non-malignant samples with EGFR highlighted. To get more information about the location of genes, check the cytoBand option to make it plotted in the Mountain plot. Then customize the marker color of tumor samples into blue.

The red circle marker highlighted where EGFR gene is in this Mountain plot. You can get it detailed information by putting your mouse on it and hold.

Example 2: Plotting Mountain plot of copy number variations on chromosome 3 of breast invasive carcinoma, head & neck squamous cell carcinoma, lung adenocarcinoma and lung squamous cell carcinoma tumor and non-malignant samples with SOX2 highlighted.

You may not like the colors and sizes of the markers plotted in default. Therefore, you can use the Figure DIY options to change the color, size and shapes of markers.

The Setting area and the final plot are shown in the following picture.

  • mountain.txt
  • Last modified: 2019/07/06 12:59
  • (external edit)