You can move about with the cd command, which stands for “change directory”. You can use it to move into a directory by specifying the path to the directory:
The heatmap will open in the viewer pane (rather than the plot pane) because it is html. You can “Show in a new window” to see it in a larger format. You can also zoom in and out and pan around the heatmap and download it as a png. You might feel the colour bars is not adding much to the plot. You can remove it by setting hide_colorbar = TRUE, in the heatmaply() function.
One of the NC replicates at time = 22 is very different from the other replicates. The CN10 treatments cluster together at high time points. CN10 samples are more similar to NC samples early on. Most of the VFAs behave similarly with highest values later in the experiment for CN10 but isohexanoate and hexanoate differ. The difference might be because isohexanoate is especially low in the NC replicates at time = 1 and hexanoate is especially high in the NC replicate 2 at time = 22
-
4. Calculate the flux - pending.
+
4. Calculate the flux
Calculate the flux(change in VFA concentration over a period of time, divided by weight or volume of material) of each VFA, by mM and by weight. Emma’s note: I think the terms flux and reaction rate are used interchangeably
I’ve requested clarification: for the flux measurements, do they need graphs of the rate of change wrt time? And is the sludge volume going to be a constant for all samples or something they measure and varies by vial?
Answer: The sludge volume is constant, at 30 mls within a 120ml vial. Some students will want to graph reaction rate with time, others will want to compare the measured GC-FID concentrations against the model output.
Calculate the flux(change in VFA concentration over a period of time, divided by weight or volume of material) of each VFA, by mM and by weight. Emma’s note: I think the terms flux and reaction rate are used interchangeably
+
The sludge volume is constant, at 30 mls. Flux units are mg vfa per ml sludge per day
+
Note: Kelly says mg/ml where earlier he used g/L. These are the same (but I called my column conc_g_l)
+
We need to use the vfa_delta_protein data frame. It contains the change in VFA concentration and the change in time. We will add a column for the flux of each VFA in g/L/day. (mg/ml/day)
+
+
sludge_volume<-30# ml
+vfa_delta_protein<-vfa_delta_protein|>
+mutate(flux =conc_g_l/delta_time/sludge_volume)
+
+
NAs at time 1 are expected because there’s no time before that to calculate a changes
+
5. Graph and extract the reaction rate
+
We can now plot the observed fluxes (reaction rates) over time
+
I’ve summarised the data to add error bars and means
To make conversions from mM to g/l we need to do mM * 0.001 * MW. We will pivot the VFA data to long format and join the molecular weight data to the VFA data. Then we can calculate the g/l. We will do this for both the cumulative and delta dataframes.
Calculate the flux(change in VFA concentration over a period of time, divided by weight or volume of material) of each VFA, by mM and by weight. Emma’s note: I think the terms flux and reaction rate are used interchangeably
+
The sludge volume is constant, at 30 mls. Flux units are mg vfa per ml sludge per day
+
Note: Kelly says mg/ml where earlier he used g/L. These are the same (but I called my column conc_g_l)
+
We need to use the vfa_delta_vfa data frame. It contains the change in VFA concentration and the change in time. We will add a column for the flux of each VFA in g/L/day. (mg/ml/day)
+
+
sludge_volume<-30# ml
+vfa_delta_vfa<-vfa_delta_vfa|>
+mutate(flux =conc_g_l/delta_time/sludge_volume)
+
+
NAs at time 1 are expected because there’s no time before that to calculate a changes
+
5. Graph and extract the reaction rate
+
We can now plot the observed fluxes (reaction rates) over time
+
I’ve summarised the data to add error bars and means