MAF | use automation framework built in the cucumber language

I am preparing my master dissertation and took the challenge of doing it all in R together with 2 students.

I used the template from Ulrik Lyngs. Modified the index.Rmd. But now all my lines are numbered...

See infra for index.Rmd code. What I had to do to make it work (build the thesis), is download MacTex and uninstall tinyTex. But I really don't know what went wrong.

I have a MetaData.csv file that contains many values to perform an analysis. All I want are: 1- Reading column names and making variables similar to column names. 2- Put values in each column into variables as an integer that can be read by other commands. column_name=Its_value

MetaData.csv:

So, i'm working with 3 different datasources in my application. Initially there were 2, but i had to add another one due to some project changes. After creating a model, a repository, a class to configure this new datasource i'm not able to start my application. It gives the error below:

I want to move the guide on the left of the plot, move it closer to the plot, I tried legend.justification = c() function in theme but it doesn't work.

I added at the end my lines and the structure of the data, I assigned the data to "plot_frame":

My code for the ggplt:

I want to move the dots underneath the plot, move them up closer to the plot, I tried position function in geol_point but it doesn't work.

I added at the end my lines and the structure of the data, I assigned the data to "plot_frame":

My code for the ggplt:

I'm still learning R, I have this dataset, it has 5 columns, first column is tracking_id, the next four columns have values of four groups.

First, I want to filter rows that have values equal or larger than 1, then I want to filter rows based on comparison of the last three columns ("CD44hi_CD69low_rep","CD44hi_CD69hi_CD103low_rep","CD44hi_CD69hi_CD103hi_rep") that are 8 folds higher or 4 folds lower compared to column ("CD44low_rep").

The output should have 5 columns, with values equal or larger than 1 that are 8 fold higher or 4 fold less of the last three column compared to second column.

I should get something like this:

To filter rows equal or larger than 1, I tried this:

I'm trying to change the dot shapes in ggplot into different shapes instead of uniformed circle shapes but keep the different colors, I see it as better visual identifier than just circles, I tried to use in geom_point, as suggested by @BenNorris (appreciation):

shape = factor(Var2))

I get this figure, I want the shapes to be implemented in the second legend, I circled these in red:

This is my code:

I'm trying to change the dot shapes in ggplot into different shapes instead of uniformed circle shapes but keep the different colors, I see it as better visual identifier than just circles, I tried to use in geom_point:

aes(shape = c(0,1,2,8))

I get an error:

I have a code in R that works. But I want to re-do it in python. I use R to use apply function in order to calculate minor allele frequency. Can someone tell me how such a code would look in python? I am using pandas to read the data in python.